diff --git a/Makefile b/Makefile
index c8b7628db..2219be02a 100644
--- a/Makefile
+++ b/Makefile
@@ -107,7 +107,7 @@ test: prepare swagger etcd-install  ## Run unit tests (add TEST=regex to specify
 	@echo "\e[33m\e[1mStarting etcd ...\e[0m"
 	@mkdir -p /tmp/aptly-etcd-data; system/t13_etcd/start-etcd.sh > /tmp/aptly-etcd-data/etcd.log 2>&1 &
 	@echo "\e[33m\e[1mRunning go test ...\e[0m"
-	faketime "$(TEST_FAKETIME)" go test -v ./... -gocheck.v=true -check.f "$(TEST)" -coverprofile=unit.out; echo $$? > .unit-test.ret
+	faketime "$(TEST_FAKETIME)" go test -timeout 20m -v ./... -gocheck.v=true -check.f "$(TEST)" -coverprofile=unit.out; echo $$? > .unit-test.ret
 	@echo "\e[33m\e[1mStopping etcd ...\e[0m"
 	@pid=`cat /tmp/etcd.pid`; kill $$pid
 	@rm -f /tmp/aptly-etcd-data/etcd.log
diff --git a/api/publish.go b/api/publish.go
index 633fdc34c..908374a71 100644
--- a/api/publish.go
+++ b/api/publish.go
@@ -465,7 +465,18 @@ func apiPublishUpdateSwitch(c *gin.Context) {
 		published.MultiDist = *b.MultiDist
 	}
 
-	resources := []string{string(published.Key())}
+	// Lock the pool prefix and all published repos sharing it to prevent cleanup race conditions.
+	// Without prefix-level locking, concurrent publishes to different distributions under the
+	// same prefix can race during cleanup, causing one operation to delete the other's files.
+	poolLockKey := fmt.Sprintf("pool:%s:%s", storage, prefix)
+	resources := []string{poolLockKey, string(published.Key())}
+	poolSiblings := collection.ByStoragePrefix(storage, prefix)
+	for _, sibling := range poolSiblings {
+		if sibling.UUID != published.UUID {
+			resources = append(resources, string(sibling.Key()))
+		}
+	}
+
 	taskName := fmt.Sprintf("Update published %s repository %s/%s", published.SourceKind, published.StoragePrefix(), published.Distribution)
 	maybeRunTaskInBackground(c, taskName, resources, func(out aptly.Progress, _ *task.Detail) (*task.ProcessReturnValue, error) {
 		err = collection.LoadComplete(published, collectionFactory)
@@ -1024,7 +1035,18 @@ func apiPublishUpdate(c *gin.Context) {
 		published.MultiDist = *b.MultiDist
 	}
 
-	resources := []string{string(published.Key())}
+	// Lock the pool prefix and all published repos sharing it to prevent cleanup race conditions.
+	// Without prefix-level locking, concurrent publishes to different distributions under the
+	// same prefix can race during cleanup, causing one operation to delete the other's files.
+	poolLockKey := fmt.Sprintf("pool:%s:%s", storage, prefix)
+	resources := []string{poolLockKey, string(published.Key())}
+	poolSiblings := collection.ByStoragePrefix(storage, prefix)
+	for _, sibling := range poolSiblings {
+		if sibling.UUID != published.UUID {
+			resources = append(resources, string(sibling.Key()))
+		}
+	}
+
 	taskName := fmt.Sprintf("Update published %s repository %s/%s", published.SourceKind, published.StoragePrefix(), published.Distribution)
 	maybeRunTaskInBackground(c, taskName, resources, func(out aptly.Progress, _ *task.Detail) (*task.ProcessReturnValue, error) {
 		result, err := published.Update(collectionFactory, out)
diff --git a/api/published_file_missing_test.go b/api/published_file_missing_test.go
new file mode 100644
index 000000000..0078c3e58
--- /dev/null
+++ b/api/published_file_missing_test.go
@@ -0,0 +1,749 @@
+package api
+
+import (
+	"bytes"
+	"encoding/json"
+	"fmt"
+	"net/http"
+	"net/http/httptest"
+	"os"
+	"os/exec"
+	"path/filepath"
+	"sync"
+	"time"
+
+	"github.com/aptly-dev/aptly/aptly"
+	ctx "github.com/aptly-dev/aptly/context"
+	"github.com/aptly-dev/aptly/deb"
+	"github.com/gin-gonic/gin"
+	"github.com/smira/flag"
+
+	. "gopkg.in/check.v1"
+)
+
+// PublishedFileMissingSuite reproduces the exact bug where:
+// - Package import succeeds
+// - Metadata is updated (Packages.gz shows the package)
+// - Publish reports success
+// - BUT the .deb file is missing from the published pool directory
+// - Result: apt-get returns 404 when trying to download the package
+type PublishedFileMissingSuite struct {
+	context    *ctx.AptlyContext
+	flags      *flag.FlagSet
+	configFile *os.File
+	router     http.Handler
+	tempDir    string
+	poolPath   string
+	publicPath string
+}
+
+var _ = Suite(&PublishedFileMissingSuite{})
+
+func (s *PublishedFileMissingSuite) SetUpSuite(c *C) {
+	aptly.Version = "publishedFileMissingTest"
+
+	tempDir, err := os.MkdirTemp("", "aptly-published-missing-test")
+	c.Assert(err, IsNil)
+	s.tempDir = tempDir
+	s.poolPath = filepath.Join(tempDir, "pool")
+	s.publicPath = filepath.Join(tempDir, "public")
+
+	file, err := os.CreateTemp("", "aptly-published-missing-config")
+	c.Assert(err, IsNil)
+	s.configFile = file
+
+	config := gin.H{
+		"rootDir":                    tempDir,
+		"downloadDir":                filepath.Join(tempDir, "download"),
+		"architectures":              []string{"amd64"},
+		"dependencyFollowSuggests":   false,
+		"dependencyFollowRecommends": false,
+		"gpgDisableSign":             true,
+		"gpgDisableVerify":           true,
+		"gpgProvider":                "internal",
+		"skipLegacyPool":             true,
+		"enableMetricsEndpoint":      false,
+	}
+
+	jsonString, err := json.Marshal(config)
+	c.Assert(err, IsNil)
+	_, err = file.Write(jsonString)
+	c.Assert(err, IsNil)
+
+	flags := flag.NewFlagSet("publishedFileMissingTestFlags", flag.ContinueOnError)
+	flags.Bool("no-lock", true, "disable database locking for test")
+	flags.Int("db-open-attempts", 3, "dummy")
+	flags.String("config", s.configFile.Name(), "config file")
+	flags.String("architectures", "", "dummy")
+	s.flags = flags
+
+	context, err := ctx.NewContext(s.flags)
+	c.Assert(err, IsNil)
+
+	s.context = context
+	s.router = Router(context)
+}
+
+func (s *PublishedFileMissingSuite) TearDownSuite(c *C) {
+	if s.configFile != nil {
+		_ = os.Remove(s.configFile.Name())
+	}
+	if s.context != nil {
+		s.context.Shutdown()
+	}
+	if s.tempDir != "" {
+		_ = os.RemoveAll(s.tempDir)
+	}
+}
+
+func (s *PublishedFileMissingSuite) SetUpTest(c *C) {
+	collectionFactory := s.context.NewCollectionFactory()
+
+	localRepoCollection := collectionFactory.LocalRepoCollection()
+	_ = localRepoCollection.ForEach(func(repo *deb.LocalRepo) error {
+		_ = localRepoCollection.Drop(repo)
+		return nil
+	})
+
+	publishedCollection := collectionFactory.PublishedRepoCollection()
+	_ = publishedCollection.ForEach(func(published *deb.PublishedRepo) error {
+		_ = publishedCollection.Remove(s.context, published.Storage, published.Prefix,
+			published.Distribution, collectionFactory, nil, true, true)
+		return nil
+	})
+}
+
+func (s *PublishedFileMissingSuite) TearDownTest(c *C) {
+	s.SetUpTest(c)
+}
+
+func (s *PublishedFileMissingSuite) httpRequest(c *C, method string, url string, body []byte) *httptest.ResponseRecorder {
+	w := httptest.NewRecorder()
+	var req *http.Request
+	var err error
+
+	if body != nil {
+		req, err = http.NewRequest(method, url, bytes.NewReader(body))
+	} else {
+		req, err = http.NewRequest(method, url, nil)
+	}
+	c.Assert(err, IsNil)
+	req.Header.Add("Content-Type", "application/json")
+	s.router.ServeHTTP(w, req)
+	return w
+}
+
+func (s *PublishedFileMissingSuite) createDebPackage(c *C, uploadID, packageName, version string) {
+	uploadPath := s.context.UploadPath()
+	uploadDir := filepath.Join(uploadPath, uploadID)
+	err := os.MkdirAll(uploadDir, 0755)
+	c.Assert(err, IsNil)
+
+	tempDir, err := os.MkdirTemp("", "deb-build")
+	c.Assert(err, IsNil)
+	defer os.RemoveAll(tempDir)
+
+	debianDir := filepath.Join(tempDir, "DEBIAN")
+	err = os.MkdirAll(debianDir, 0755)
+	c.Assert(err, IsNil)
+
+	controlContent := fmt.Sprintf(`Package: %s
+Version: %s
+Section: libs
+Priority: optional
+Architecture: amd64
+Maintainer: Test <test@example.com>
+Description: Test package
+ Test package for published file missing bug.
+`, packageName, version)
+
+	err = os.WriteFile(filepath.Join(debianDir, "control"), []byte(controlContent), 0644)
+	c.Assert(err, IsNil)
+
+	usrDir := filepath.Join(tempDir, "usr", "lib")
+	err = os.MkdirAll(usrDir, 0755)
+	c.Assert(err, IsNil)
+	err = os.WriteFile(filepath.Join(usrDir, "lib.so"), []byte("library"), 0644)
+	c.Assert(err, IsNil)
+
+	debFile := filepath.Join(uploadDir, fmt.Sprintf("%s_%s_amd64.deb", packageName, version))
+	cmd := exec.Command("dpkg-deb", "--build", tempDir, debFile)
+	err = cmd.Run()
+	c.Assert(err, IsNil)
+}
+
+// TestPublishedFileGoMissing reproduces the exact production bug
+func (s *PublishedFileMissingSuite) TestPublishedFileGoMissing(c *C) {
+	c.Log("=== Reproducing: Package in metadata but 404 on download ===")
+
+	// Create and publish a repository
+	repoName := "test-repo"
+	distribution := "bullseye"
+
+	createBody, _ := json.Marshal(gin.H{
+		"Name":                repoName,
+		"DefaultDistribution": distribution,
+		"DefaultComponent":    "main",
+	})
+	resp := s.httpRequest(c, "POST", "/api/repos", createBody)
+	c.Assert(resp.Code, Equals, 201, Commentf("Failed to create repo: %s", resp.Body.String()))
+
+	publishBody, _ := json.Marshal(gin.H{
+		"SourceKind":    "local",
+		"Distribution":  distribution,
+		"Architectures": []string{"amd64"},
+		"Sources": []gin.H{
+			{"Component": "main", "Name": repoName},
+		},
+		"Signing": gin.H{"Skip": true},
+	})
+	resp = s.httpRequest(c, "POST", "/api/publish/hrt", publishBody)
+	c.Assert(resp.Code, Equals, 201, Commentf("Failed to publish: %s", resp.Body.String()))
+
+	// Create package
+	packageName := "hrt-libblobbyclient1"
+	version := "20250926.152427+hrtdeb11"
+	uploadID := "test-upload-1"
+
+	s.createDebPackage(c, uploadID, packageName, version)
+
+	// Add package
+	resp = s.httpRequest(c, "POST", fmt.Sprintf("/api/repos/%s/file/%s?noRemove=0", repoName, uploadID), nil)
+	c.Assert(resp.Code, Equals, 200, Commentf("Failed to add package: %s", resp.Body.String()))
+
+	// Update publish
+	updateBody, _ := json.Marshal(gin.H{
+		"Signing":        gin.H{"Skip": true},
+		"ForceOverwrite": true,
+	})
+	resp = s.httpRequest(c, "PUT", fmt.Sprintf("/api/publish/hrt/%s", distribution), updateBody)
+	c.Assert(resp.Code, Equals, 200, Commentf("Failed to update publish: %s", resp.Body.String()))
+
+	// Now check if the file is actually accessible in the published location
+	publishedStorage := s.context.GetPublishedStorage("")
+	publicPath := publishedStorage.(aptly.FileSystemPublishedStorage).PublicPath()
+
+	// Expected file path: hrt/pool/main/h/hrt-libblobbyclient1/hrt-libblobbyclient1_20250926.152427+hrtdeb11_amd64.deb
+	expectedPath := filepath.Join(publicPath, "hrt", "pool", "main", "h", packageName,
+		fmt.Sprintf("%s_%s_amd64.deb", packageName, version))
+
+	c.Logf("Checking for published file at: %s", expectedPath)
+
+	fileInfo, err := os.Stat(expectedPath)
+	fileExists := err == nil
+
+	c.Logf("File exists: %v", fileExists)
+	if fileExists {
+		c.Logf("File size: %d bytes", fileInfo.Size())
+	}
+
+	// Check metadata
+	resp = s.httpRequest(c, "GET", fmt.Sprintf("/api/repos/%s/packages", repoName), nil)
+	var packages []string
+	err = json.Unmarshal(resp.Body.Bytes(), &packages)
+	c.Assert(err, IsNil)
+	c.Logf("Packages in metadata: %d", len(packages))
+
+	// THE BUG: Metadata says package exists, but file is missing from published location
+	if len(packages) > 0 && !fileExists {
+		c.Logf("★★★ BUG REPRODUCED! ★★★")
+		c.Logf("Metadata shows %d package(s) but file is missing at: %s", len(packages), expectedPath)
+		c.Logf("This is exactly what causes: 404 Not Found [IP: 10.20.72.62 3142]")
+
+		c.Fatal("BUG CONFIRMED: Package in metadata but missing from published directory!")
+	}
+
+	c.Assert(fileExists, Equals, true, Commentf(
+		"Published file should exist at %s when package is in metadata", expectedPath))
+}
+
+// TestConcurrentPublishRace tries to trigger the race with concurrent publishes
+func (s *PublishedFileMissingSuite) TestConcurrentPublishRace(c *C) {
+	c.Log("=== Testing concurrent publish race condition ===")
+
+	const numIterations = 4
+
+	for iteration := 0; iteration < numIterations; iteration++ {
+		c.Logf("--- Iteration %d/%d ---", iteration+1, numIterations)
+
+		// Create repo
+		repoName := fmt.Sprintf("race-repo-%d", iteration)
+		distribution := fmt.Sprintf("dist-%d", iteration)
+
+		createBody, _ := json.Marshal(gin.H{
+			"Name":                repoName,
+			"DefaultDistribution": distribution,
+			"DefaultComponent":    "main",
+		})
+		resp := s.httpRequest(c, "POST", "/api/repos", createBody)
+		c.Assert(resp.Code, Equals, 201)
+
+		publishBody, _ := json.Marshal(gin.H{
+			"SourceKind":    "local",
+			"Distribution":  distribution,
+			"Architectures": []string{"amd64"},
+			"Sources": []gin.H{
+				{"Component": "main", "Name": repoName},
+			},
+			"Signing": gin.H{"Skip": true},
+		})
+		resp = s.httpRequest(c, "POST", "/api/publish/concurrent", publishBody)
+		c.Assert(resp.Code, Equals, 201)
+
+		// Create multiple packages
+		var wg sync.WaitGroup
+		numPackages := 5
+
+		for i := 0; i < numPackages; i++ {
+			wg.Add(1)
+			go func(idx int) {
+				defer wg.Done()
+
+				packageName := fmt.Sprintf("pkg-%d-%d", iteration, idx)
+				version := "1.0.0"
+				uploadID := fmt.Sprintf("upload-%d-%d", iteration, idx)
+
+				s.createDebPackage(c, uploadID, packageName, version)
+
+				// Add package
+				resp := s.httpRequest(c, "POST", fmt.Sprintf("/api/repos/%s/file/%s?noRemove=0", repoName, uploadID), nil)
+				c.Logf("Package %d add: %d", idx, resp.Code)
+
+				// Small delay
+				time.Sleep(time.Duration(5+idx*2) * time.Millisecond)
+
+				// Publish
+				updateBody, _ := json.Marshal(gin.H{
+					"Signing":        gin.H{"Skip": true},
+					"ForceOverwrite": true,
+				})
+				resp = s.httpRequest(c, "PUT", fmt.Sprintf("/api/publish/concurrent/%s", distribution), updateBody)
+				c.Logf("Publish %d: %d", idx, resp.Code)
+			}(i)
+		}
+
+		wg.Wait()
+		time.Sleep(100 * time.Millisecond)
+
+		// Check all packages
+		resp = s.httpRequest(c, "GET", fmt.Sprintf("/api/repos/%s/packages", repoName), nil)
+		var packages []string
+		err := json.Unmarshal(resp.Body.Bytes(), &packages)
+		c.Assert(err, IsNil)
+
+		// Check published files
+		publishedStorage := s.context.GetPublishedStorage("")
+		publicPath := publishedStorage.(aptly.FileSystemPublishedStorage).PublicPath()
+
+		missingFiles := []string{}
+		for i := 0; i < numPackages; i++ {
+			packageName := fmt.Sprintf("pkg-%d-%d", iteration, i)
+			version := "1.0.0"
+
+			// Calculate pool path
+			poolSubdir := string(packageName[0])
+			expectedPath := filepath.Join(publicPath, "concurrent", "pool", "main", poolSubdir, packageName,
+				fmt.Sprintf("%s_%s_amd64.deb", packageName, version))
+
+			if _, err := os.Stat(expectedPath); os.IsNotExist(err) {
+				missingFiles = append(missingFiles, expectedPath)
+			}
+		}
+
+		if len(missingFiles) > 0 {
+			c.Logf("★★★ BUG DETECTED in iteration %d/%d! ★★★", iteration+1, numIterations)
+			c.Logf("Metadata shows %d packages, but %d files are MISSING:", len(packages), len(missingFiles))
+			for i, f := range missingFiles {
+				c.Logf("  [iter %d] File MISSING %d/%d: %s", iteration+1, i+1, len(missingFiles), f)
+			}
+
+			c.Fatalf("BUG REPRODUCED in iteration %d/%d: %d published files missing", iteration+1, numIterations, len(missingFiles))
+		} else {
+			c.Logf("[iter %d/%d] All %d files present - OK", iteration+1, numIterations, numPackages)
+		}
+	}
+
+	c.Logf("All %d iterations passed - bug not reproduced with current timing", numIterations)
+}
+
+// TestIdenticalPackageRace tests the specific case of identical SHA256 packages
+func (s *PublishedFileMissingSuite) TestIdenticalPackageRace(c *C) {
+	c.Log("=== AGGRESSIVE test: identical package (same SHA256) race ===")
+
+	const numIterations = 4
+	packageName := "shared-package"
+
+	for iter := 0; iter < numIterations; iter++ {
+		c.Logf("Iteration %d/%d", iter+1, numIterations)
+
+		// Create two repos that will get the SAME package (unique per iteration)
+		repos := []string{fmt.Sprintf("identical-a-%d", iter), fmt.Sprintf("identical-b-%d", iter)}
+		dists := []string{fmt.Sprintf("dist-a-%d", iter), fmt.Sprintf("dist-b-%d", iter)}
+
+		for i := range repos {
+			createBody, _ := json.Marshal(gin.H{
+				"Name":                repos[i],
+				"DefaultDistribution": dists[i],
+				"DefaultComponent":    "main",
+			})
+			resp := s.httpRequest(c, "POST", "/api/repos", createBody)
+			c.Assert(resp.Code, Equals, 201)
+
+			publishBody, _ := json.Marshal(gin.H{
+				"SourceKind":    "local",
+				"Distribution":  dists[i],
+				"Architectures": []string{"amd64"},
+				"Sources": []gin.H{
+					{"Component": "main", "Name": repos[i]},
+				},
+				"Signing": gin.H{"Skip": true},
+				"SkipBz2": true,
+			})
+			resp = s.httpRequest(c, "POST", "/api/publish/identical", publishBody)
+			c.Assert(resp.Code, Equals, 201)
+		}
+
+		// Create IDENTICAL package file with UNIQUE VERSION per iteration
+		version := fmt.Sprintf("1.0.%d", iter)
+		uploadID1 := fmt.Sprintf("identical-upload-1-%d", iter)
+		uploadID2 := fmt.Sprintf("identical-upload-2-%d", iter)
+
+		s.createDebPackage(c, uploadID1, packageName, version)
+
+		// Copy to second upload (same SHA256)
+		uploadPath := s.context.UploadPath()
+		src := filepath.Join(uploadPath, uploadID1, fmt.Sprintf("%s_%s_amd64.deb", packageName, version))
+		destDir := filepath.Join(uploadPath, uploadID2)
+		err := os.MkdirAll(destDir, 0755)
+		c.Assert(err, IsNil)
+		dest := filepath.Join(destDir, fmt.Sprintf("%s_%s_amd64.deb", packageName, version))
+
+		srcData, readErr := os.ReadFile(src)
+		c.Assert(readErr, IsNil)
+		err = os.WriteFile(dest, srcData, 0644)
+		c.Assert(err, IsNil)
+
+		// Race: add and publish both simultaneously
+		var wg sync.WaitGroup
+		wg.Add(4)
+
+		go func() {
+			defer wg.Done()
+			time.Sleep(5 * time.Millisecond)
+			resp := s.httpRequest(c, "POST", fmt.Sprintf("/api/repos/%s/file/%s?noRemove=0", repos[0], uploadID1), nil)
+			c.Logf("[iter %d] Import A complete: %d", iter, resp.Code)
+		}()
+
+		go func() {
+			defer wg.Done()
+			time.Sleep(7 * time.Millisecond)
+			resp := s.httpRequest(c, "POST", fmt.Sprintf("/api/repos/%s/file/%s?noRemove=0", repos[1], uploadID2), nil)
+			c.Logf("[iter %d] Import B complete: %d", iter, resp.Code)
+		}()
+
+		go func() {
+			defer wg.Done()
+			time.Sleep(15 * time.Millisecond)
+			updateBody, _ := json.Marshal(gin.H{"Signing": gin.H{"Skip": true}, "ForceOverwrite": true, "SkipBz2": true})
+			resp := s.httpRequest(c, "PUT", fmt.Sprintf("/api/publish/identical/%s", dists[0]), updateBody)
+			c.Logf("[iter %d] Publish A complete: %d", iter, resp.Code)
+		}()
+
+		go func() {
+			defer wg.Done()
+			time.Sleep(18 * time.Millisecond)
+			updateBody, _ := json.Marshal(gin.H{"Signing": gin.H{"Skip": true}, "ForceOverwrite": true, "SkipBz2": true})
+			resp := s.httpRequest(c, "PUT", fmt.Sprintf("/api/publish/identical/%s", dists[1]), updateBody)
+			c.Logf("[iter %d] Publish B complete: %d", iter, resp.Code)
+		}()
+
+		wg.Wait()
+		time.Sleep(200 * time.Millisecond)
+		c.Logf("[iter %d] All operations complete", iter)
+
+		// Check the shared pool location
+		publishedStorage := s.context.GetPublishedStorage("")
+		publicPath := publishedStorage.(aptly.FileSystemPublishedStorage).PublicPath()
+
+		poolSubdir := string(packageName[0])
+		sharedPoolPath := filepath.Join(publicPath, "identical", "pool", "main", poolSubdir, packageName,
+			fmt.Sprintf("%s_%s_amd64.deb", packageName, version))
+
+		fileInfo, err := os.Stat(sharedPoolPath)
+		fileExists := err == nil
+
+		if fileExists {
+			c.Logf("[iter %d] File EXISTS at %s (size: %d)", iter, sharedPoolPath, fileInfo.Size())
+		} else {
+			c.Logf("[iter %d] File MISSING at %s (error: %v)", iter, sharedPoolPath, err)
+		}
+
+		// Check metadata
+		var packagesA, packagesB []string
+		resp := s.httpRequest(c, "GET", fmt.Sprintf("/api/repos/%s/packages", repos[0]), nil)
+		err = json.Unmarshal(resp.Body.Bytes(), &packagesA)
+		c.Assert(err, IsNil)
+		resp = s.httpRequest(c, "GET", fmt.Sprintf("/api/repos/%s/packages", repos[1]), nil)
+		err = json.Unmarshal(resp.Body.Bytes(), &packagesB)
+		c.Assert(err, IsNil)
+
+		c.Logf("[iter %d] Packages in metadata: A=%d, B=%d", iter, len(packagesA), len(packagesB))
+
+		// THE BUG: Both repos show packages in metadata, but the shared pool file is missing
+		if (len(packagesA) > 0 || len(packagesB) > 0) && !fileExists {
+			c.Logf("★★★ BUG REPRODUCED in iteration %d! ★★★", iter+1)
+			c.Logf("Packages in metadata A: %d, B: %d", len(packagesA), len(packagesB))
+			c.Logf("Shared pool file exists: %v", fileExists)
+			c.Logf("Pool path: %s", sharedPoolPath)
+
+			// List what files ARE in the pool directory
+			poolDir := filepath.Dir(sharedPoolPath)
+			if entries, err := os.ReadDir(poolDir); err == nil {
+				c.Logf("Files in pool directory %s:", poolDir)
+				for _, entry := range entries {
+					c.Logf("  - %s", entry.Name())
+				}
+			}
+
+			c.Fatalf("Metadata shows packages but shared pool file is missing (iteration %d)", iter+1)
+		}
+	}
+
+	c.Logf("All %d iterations passed - bug not reproduced", numIterations)
+}
+
+// TestConcurrentSnapshotPublishToSamePrefix reproduces the EXACT production bug:
+// Multiple snapshots are published concurrently to the SAME prefix but different distributions.
+// Example from production logs:
+//   - trixie-pgdg published to "external/postgres-auto/trixie"
+//   - bullseye-pgdg published to "external/postgres-auto/bullseye"
+// Both share the same pool directory, causing cleanup race conditions.
+func (s *PublishedFileMissingSuite) TestConcurrentSnapshotPublishToSamePrefix(c *C) {
+	const numIterations = 4
+
+	for iter := 0; iter < numIterations; iter++ {
+		c.Logf("--- Iteration %d/%d ---", iter+1, numIterations)
+
+		// Create two repos with different packages (simulating trixie-pgdg and bullseye-pgdg)
+		repoTrixie := fmt.Sprintf("trixie-pgdg-%d", iter)
+		repoBullseye := fmt.Sprintf("bullseye-pgdg-%d", iter)
+
+		// Create trixie repo
+		createBody, _ := json.Marshal(gin.H{
+			"Name":                repoTrixie,
+			"DefaultDistribution": "trixie",
+			"DefaultComponent":    "main",
+		})
+		resp := s.httpRequest(c, "POST", "/api/repos", createBody)
+		c.Assert(resp.Code, Equals, 201, Commentf("Failed to create trixie repo"))
+
+		// Create bullseye repo
+		createBody, _ = json.Marshal(gin.H{
+			"Name":                repoBullseye,
+			"DefaultDistribution": "bullseye",
+			"DefaultComponent":    "main",
+		})
+		resp = s.httpRequest(c, "POST", "/api/repos", createBody)
+		c.Assert(resp.Code, Equals, 201, Commentf("Failed to create bullseye repo"))
+
+		// Add packages to both repos
+		numPackages := 3
+
+		// Add packages to trixie repo
+		for i := 0; i < numPackages; i++ {
+			packageName := fmt.Sprintf("postgresql-17-trixie-pkg%d", i)
+			version := fmt.Sprintf("17.0.%d", iter)
+			uploadID := fmt.Sprintf("trixie-upload-%d-%d", iter, i)
+
+			s.createDebPackage(c, uploadID, packageName, version)
+			resp = s.httpRequest(c, "POST", fmt.Sprintf("/api/repos/%s/file/%s?noRemove=0", repoTrixie, uploadID), nil)
+			c.Assert(resp.Code, Equals, 200, Commentf("Failed to add package to trixie"))
+		}
+
+		// Add packages to bullseye repo
+		for i := 0; i < numPackages; i++ {
+			packageName := fmt.Sprintf("postgresql-17-bullseye-pkg%d", i)
+			version := fmt.Sprintf("17.0.%d", iter)
+			uploadID := fmt.Sprintf("bullseye-upload-%d-%d", iter, i)
+
+			s.createDebPackage(c, uploadID, packageName, version)
+			resp = s.httpRequest(c, "POST", fmt.Sprintf("/api/repos/%s/file/%s?noRemove=0", repoBullseye, uploadID), nil)
+			c.Assert(resp.Code, Equals, 200, Commentf("Failed to add package to bullseye"))
+		}
+
+		// Create snapshots from both repos
+		snapshotTrixie := fmt.Sprintf("%s-snap", repoTrixie)
+		snapshotBullseye := fmt.Sprintf("%s-snap", repoBullseye)
+
+		createSnapshotBody, _ := json.Marshal(gin.H{"Name": snapshotTrixie})
+		resp = s.httpRequest(c, "POST", fmt.Sprintf("/api/repos/%s/snapshots", repoTrixie), createSnapshotBody)
+		c.Assert(resp.Code, Equals, 201, Commentf("Failed to create trixie snapshot"))
+
+		createSnapshotBody, _ = json.Marshal(gin.H{"Name": snapshotBullseye})
+		resp = s.httpRequest(c, "POST", fmt.Sprintf("/api/repos/%s/snapshots", repoBullseye), createSnapshotBody)
+		c.Assert(resp.Code, Equals, 201, Commentf("Failed to create bullseye snapshot"))
+
+		// Publish both snapshots CONCURRENTLY to the SAME prefix
+		// This mimics production where both are published to "external/postgres-auto"
+		// Use the SAME prefix across all iterations to trigger the race more aggressively
+		sharedPrefix := "postgres-auto"
+
+		var wg sync.WaitGroup
+		var trixiePublishCode, bullseyePublishCode int
+
+		wg.Add(2)
+
+		// Publish or update trixie snapshot
+		go func() {
+			defer wg.Done()
+
+			var resp *httptest.ResponseRecorder
+			if iter == 0 {
+				// First iteration: CREATE
+				publishBody, _ := json.Marshal(gin.H{
+					"SourceKind":    "snapshot",
+					"Distribution":  "trixie",
+					"Architectures": []string{"amd64"},
+					"Sources": []gin.H{
+						{"Name": snapshotTrixie},
+					},
+					"Signing":        gin.H{"Skip": true},
+					"SkipBz2":        true,
+					"ForceOverwrite": true,
+					"SkipCleanup":    false, // Force cleanup to run
+				})
+				resp = s.httpRequest(c, "POST", fmt.Sprintf("/api/publish/%s", sharedPrefix), publishBody)
+			} else {
+				// Subsequent iterations: UPDATE (this is what happens in production)
+				updateBody, _ := json.Marshal(gin.H{
+					"Snapshots": []gin.H{
+						{"Component": "main", "Name": snapshotTrixie},
+					},
+					"Signing":        gin.H{"Skip": true},
+					"SkipBz2":        true,
+					"ForceOverwrite": true,
+					"SkipCleanup":    false,
+				})
+				resp = s.httpRequest(c, "PUT", fmt.Sprintf("/api/publish/%s/trixie", sharedPrefix), updateBody)
+			}
+			trixiePublishCode = resp.Code
+			c.Logf("[iter %d] Trixie publish/update completed: %d", iter, resp.Code)
+		}()
+
+		// Publish or update bullseye snapshot
+		go func() {
+			defer wg.Done()
+
+			var resp *httptest.ResponseRecorder
+			if iter == 0 {
+				// First iteration: CREATE
+				publishBody, _ := json.Marshal(gin.H{
+					"SourceKind":    "snapshot",
+					"Distribution":  "bullseye",
+					"Architectures": []string{"amd64"},
+					"Sources": []gin.H{
+						{"Name": snapshotBullseye},
+					},
+					"Signing":        gin.H{"Skip": true},
+					"SkipBz2":        true,
+					"ForceOverwrite": true,
+					"SkipCleanup":    false,
+				})
+				resp = s.httpRequest(c, "POST", fmt.Sprintf("/api/publish/%s", sharedPrefix), publishBody)
+			} else {
+				// Subsequent iterations: UPDATE
+				updateBody, _ := json.Marshal(gin.H{
+					"Snapshots": []gin.H{
+						{"Component": "main", "Name": snapshotBullseye},
+					},
+					"Signing":        gin.H{"Skip": true},
+					"SkipBz2":        true,
+					"ForceOverwrite": true,
+					"SkipCleanup":    false,
+				})
+				resp = s.httpRequest(c, "PUT", fmt.Sprintf("/api/publish/%s/bullseye", sharedPrefix), updateBody)
+			}
+			bullseyePublishCode = resp.Code
+			c.Logf("[iter %d] Bullseye publish/update completed: %d", iter, resp.Code)
+		}()
+
+		wg.Wait()
+		time.Sleep(50 * time.Millisecond)
+
+		// Verify publishes succeeded (201 for create, 200 for update)
+		expectedCode := 201
+		if iter > 0 {
+			expectedCode = 200
+		}
+		c.Assert(trixiePublishCode, Equals, expectedCode, Commentf("Trixie publish/update should succeed"))
+		c.Assert(bullseyePublishCode, Equals, expectedCode, Commentf("Bullseye publish/update should succeed"))
+
+		// Verify ALL package files exist in the published pool
+		publishedStorage := s.context.GetPublishedStorage("")
+		publicPath := publishedStorage.(aptly.FileSystemPublishedStorage).PublicPath()
+
+		missingFiles := []string{}
+		expectedFiles := []string{}
+
+		// Check trixie packages
+		for i := 0; i < numPackages; i++ {
+			packageName := fmt.Sprintf("postgresql-17-trixie-pkg%d", i)
+			version := fmt.Sprintf("17.0.%d", iter)
+
+			poolSubdir := string(packageName[0])
+			expectedPath := filepath.Join(publicPath, sharedPrefix, "pool", "main", poolSubdir, packageName,
+				fmt.Sprintf("%s_%s_amd64.deb", packageName, version))
+
+			expectedFiles = append(expectedFiles, expectedPath)
+			if _, err := os.Stat(expectedPath); os.IsNotExist(err) {
+				missingFiles = append(missingFiles, fmt.Sprintf("TRIXIE: %s", filepath.Base(expectedPath)))
+			}
+		}
+
+		// Check bullseye packages
+		for i := 0; i < numPackages; i++ {
+			packageName := fmt.Sprintf("postgresql-17-bullseye-pkg%d", i)
+			version := fmt.Sprintf("17.0.%d", iter)
+
+			poolSubdir := string(packageName[0])
+			expectedPath := filepath.Join(publicPath, sharedPrefix, "pool", "main", poolSubdir, packageName,
+				fmt.Sprintf("%s_%s_amd64.deb", packageName, version))
+
+			expectedFiles = append(expectedFiles, expectedPath)
+			if _, err := os.Stat(expectedPath); os.IsNotExist(err) {
+				missingFiles = append(missingFiles, fmt.Sprintf("BULLSEYE: %s", filepath.Base(expectedPath)))
+			}
+		}
+
+		// BUG: Files from one distribution are deleted by the other's cleanup
+		if len(missingFiles) > 0 {
+			c.Logf("★★★ BUG REPRODUCED in iteration %d/%d! ★★★", iter+1, numIterations)
+			c.Logf("Both publishes to prefix '%s' succeeded, but %d files are MISSING:", sharedPrefix, len(missingFiles))
+			for i, f := range missingFiles {
+				c.Logf("  Missing file %d/%d: %s", i+1, len(missingFiles), f)
+			}
+
+			c.Logf("\nThis reproduces the exact production bug where:")
+			c.Logf("  1. Mirror updates complete successfully")
+			c.Logf("  2. Snapshots are created")
+			c.Logf("  3. Both snapshots publish to same prefix (different distributions)")
+			c.Logf("  4. Cleanup from one publish DELETES files from the other")
+			c.Logf("  5. Result: apt-get returns 404 when downloading packages")
+
+			// List what's actually in the pool
+			poolDir := filepath.Join(publicPath, sharedPrefix, "pool", "main")
+			if entries, err := os.ReadDir(poolDir); err == nil {
+				c.Logf("\nActual pool directory contents (%s):", poolDir)
+				for _, entry := range entries {
+					c.Logf("  - %s/", entry.Name())
+				}
+			}
+
+			c.Fatalf("BUG CONFIRMED (iteration %d/%d): %d files missing from shared pool",
+				iter+1, numIterations, len(missingFiles))
+		} else {
+			c.Logf("[iter %d/%d] All %d files present - OK", iter+1, numIterations, len(expectedFiles))
+		}
+	}
+	c.Logf("✓ All %d iterations passed - no files missing", numIterations)
+}
diff --git a/api/repos.go b/api/repos.go
index ff496f2cd..28c0b5090 100644
--- a/api/repos.go
+++ b/api/repos.go
@@ -511,6 +511,13 @@ func apiReposPackageFromDir(c *gin.Context) {
 		return
 	}
 
+	// When adding packages to a local repo, we need to prevent concurrent publish operations
+	// from reading stale data. To do this, we find all published repositories that use this
+	// local repo and include them in the resource lock set. This ensures the task system
+	// will serialize package additions and publishes, preventing race conditions.
+	publishedCollection := collectionFactory.PublishedRepoCollection()
+	publishedRepos := publishedCollection.ByLocalRepo(repo)
+
 	var taskName string
 	var sources []string
 	if fileParam == "" {
@@ -521,7 +528,14 @@ func apiReposPackageFromDir(c *gin.Context) {
 		taskName = fmt.Sprintf("Add package %s from dir %s to repo %s", fileParam, dirParam, name)
 	}
 
+	// Build the resource lock list: start with the local repo itself
 	resources := []string{string(repo.Key())}
+
+	// Add all published repos that reference this local repo to the lock list
+	for _, published := range publishedRepos {
+		resources = append(resources, string(published.Key()))
+	}
+
 	resources = append(resources, sources...)
 	maybeRunTaskInBackground(c, taskName, resources, func(out aptly.Progress, _ *task.Detail) (*task.ProcessReturnValue, error) {
 		err = collection.LoadComplete(repo)
diff --git a/deb/publish.go b/deb/publish.go
index 46c9557f2..165c12ecc 100644
--- a/deb/publish.go
+++ b/deb/publish.go
@@ -1436,6 +1436,19 @@ func (collection *PublishedRepoCollection) ByLocalRepo(repo *LocalRepo) []*Publi
 	return result
 }
 
+// ByStoragePrefix looks up all repositories with the same storage and prefix
+func (collection *PublishedRepoCollection) ByStoragePrefix(storage, prefix string) []*PublishedRepo {
+	collection.loadList()
+
+	var result []*PublishedRepo
+	for _, r := range collection.list {
+		if r.Storage == storage && r.Prefix == prefix {
+			result = append(result, r)
+		}
+	}
+	return result
+}
+
 // ForEach runs method for each repository
 func (collection *PublishedRepoCollection) ForEach(handler func(*PublishedRepo) error) error {
 	return collection.db.ProcessByPrefix([]byte("U"), func(_, blob []byte) error {
@@ -1459,7 +1472,6 @@ func (collection *PublishedRepoCollection) Len() int {
 func (collection *PublishedRepoCollection) listReferencedFilesByComponent(prefix string, components []string,
 	collectionFactory *CollectionFactory, progress aptly.Progress) (map[string][]string, error) {
 	referencedFiles := map[string][]string{}
-	processedComponentRefs := map[string]*PackageRefList{}
 
 	for _, r := range collection.list {
 		if r.Prefix == prefix && !r.MultiDist {
@@ -1484,20 +1496,17 @@ func (collection *PublishedRepoCollection) listReferencedFilesByComponent(prefix
 
 			for _, component := range components {
 				if utils.StrSliceHasItem(repoComponents, component) {
-					unseenRefs := r.RefList(component)
-					processedRefs := processedComponentRefs[component]
-					if processedRefs != nil {
-						unseenRefs = unseenRefs.Subtract(processedRefs)
-					} else {
-						processedRefs = NewPackageRefList()
-					}
+					refList := r.RefList(component)
+
+					// Process all package refs without subtracting previously seen ones.
+					// Subtraction was an optimization to avoid duplicate processing, but it caused
+					// shared files between distributions to be incorrectly marked as orphaned during cleanup.
 
-					if unseenRefs.Len() == 0 {
+					if refList.Len() == 0 {
 						continue
 					}
-					processedComponentRefs[component] = processedRefs.Merge(unseenRefs, false, true)
 
-					packageList, err := NewPackageListFromRefList(unseenRefs, collectionFactory.PackageCollection(), progress)
+					packageList, err := NewPackageListFromRefList(refList, collectionFactory.PackageCollection(), progress)
 					if err != nil {
 						return nil, err
 					}
@@ -1528,6 +1537,8 @@ func (collection *PublishedRepoCollection) CleanupPrefixComponentFiles(published
 
 	var err error
 
+	// Force reload to see recent database commits before cleanup.
+	collection.list = nil
 	collection.loadList()
 
 	storage := published.Storage
@@ -1696,6 +1707,20 @@ func (collection *PublishedRepoCollection) Remove(publishedStorageProvider aptly
 		// ignore error with -force-drop
 	}
 
+	// Delete from database first before cleanup to ensure cleanup sees the updated state
+	batch := collection.db.CreateBatch()
+	_ = batch.Delete(repo.Key())
+
+	for _, component := range repo.Components() {
+		_ = batch.Delete(repo.RefKey(component))
+	}
+
+	err = batch.Write()
+	if err != nil {
+		return err
+	}
+
+	// Remove from in-memory list after database commit
 	collection.list[len(collection.list)-1], collection.list[repoPosition], collection.list =
 		nil, collection.list[len(collection.list)-1], collection.list[:len(collection.list)-1]
 
@@ -1708,12 +1733,5 @@ func (collection *PublishedRepoCollection) Remove(publishedStorageProvider aptly
 		}
 	}
 
-	batch := collection.db.CreateBatch()
-	_ = batch.Delete(repo.Key())
-
-	for _, component := range repo.Components() {
-		_ = batch.Delete(repo.RefKey(component))
-	}
-
-	return batch.Write()
+	return nil
 }
diff --git a/deb/publish_test.go b/deb/publish_test.go
index 0bfa08d7c..9a867245c 100644
--- a/deb/publish_test.go
+++ b/deb/publish_test.go
@@ -756,7 +756,8 @@ func (s *PublishedRepoCollectionSuite) TestListReferencedFiles(c *C) {
 	snap3 := NewSnapshotFromRefList("snap3", []*Snapshot{}, s.snap2.RefList(), "desc3")
 	_ = s.snapshotCollection.Add(snap3)
 
-	// Ensure that adding a second publish point with matching files doesn't give duplicate results.
+	// When a second publish point references the same files, they should be listed for each repo
+	// to ensure cleanup doesn't delete files still referenced by other distributions.
 	repo3, err := NewPublishedRepo("", "", "anaconda-2", []string{}, []string{"main"}, []interface{}{snap3}, s.factory, false)
 	c.Check(err, IsNil)
 	c.Check(s.collection.Add(repo3), IsNil)
@@ -771,7 +772,10 @@ func (s *PublishedRepoCollectionSuite) TestListReferencedFiles(c *C) {
 			"a/alien-arena/alien-arena-common_7.40-2_i386.deb",
 			"a/alien-arena/mars-invaders_7.40-2_i386.deb",
 		},
-		"main": {"a/alien-arena/lonely-strangers_7.40-2_i386.deb"},
+		"main": {
+			"a/alien-arena/lonely-strangers_7.40-2_i386.deb",
+			"a/alien-arena/lonely-strangers_7.40-2_i386.deb",
+		},
 	})
 }