diff --git a/cmd/db_recover.go b/cmd/db_recover.go
index baf599c51..2aa621d21 100644
--- a/cmd/db_recover.go
+++ b/cmd/db_recover.go
@@ -57,20 +57,37 @@ func checkRepo(repo *deb.LocalRepo) error {
 
 	err := repos.LoadComplete(repo)
 	if err != nil {
-		return fmt.Errorf("load complete repo %q: %s", repo.Name, err)
+		// If we can't load the repo, it might be severely corrupted
+		// Log the error but continue with other repos
+		context.Progress().Printf("Warning: Cannot load repo %q: %s\n", repo.Name, err)
+		return nil
 	}
 
-	dangling, err := deb.FindDanglingReferences(repo.RefList(), collectionFactory.PackageCollection())
+	// Check if RefList is nil (severe corruption case)
+	refList := repo.RefList()
+	if refList == nil {
+		context.Progress().Printf("Warning: Repo %q has no reference list (severely corrupted), initializing empty list\n", repo.Name)
+		// Initialize with empty reflist
+		repo.UpdateRefList(deb.NewPackageRefList())
+		if err = repos.Update(repo); err != nil {
+			return fmt.Errorf("update repo with empty reflist: %w", err)
+		}
+		return nil
+	}
+
+	dangling, err := deb.FindDanglingReferences(refList, collectionFactory.PackageCollection())
 	if err != nil {
-		return fmt.Errorf("find dangling references: %w", err)
+		// If we can't find dangling references, log but continue
+		context.Progress().Printf("Warning: Cannot check dangling references for repo %q: %s\n", repo.Name, err)
+		return nil
 	}
 
-	if len(dangling.Refs) > 0 {
+	if dangling != nil && len(dangling.Refs) > 0 {
 		for _, ref := range dangling.Refs {
 			context.Progress().Printf("Removing dangling database reference %q\n", ref)
 		}
 
-		repo.UpdateRefList(repo.RefList().Subtract(dangling))
+		repo.UpdateRefList(refList.Subtract(dangling))
 
 		if err = repos.Update(repo); err != nil {
 			return fmt.Errorf("update repo: %w", err)
diff --git a/deb/local.go b/deb/local.go
index 4be460769..f4c6e39d8 100644
--- a/deb/local.go
+++ b/deb/local.go
@@ -160,9 +160,15 @@ func (collection *LocalRepoCollection) Add(repo *LocalRepo) error {
 func (collection *LocalRepoCollection) Update(repo *LocalRepo) error {
 	batch := collection.db.CreateBatch()
 	_ = batch.Put(repo.Key(), repo.Encode())
+
 	if repo.packageRefs != nil {
 		_ = batch.Put(repo.RefKey(), repo.packageRefs.Encode())
+	} else {
+		// Delete RefKey if packageRefs is nil
+		// This prevents inconsistent state where RefKey exists but is corrupted
+		_ = batch.Delete(repo.RefKey())
 	}
+
 	return batch.Write()
 }
 
diff --git a/deb/remote.go b/deb/remote.go
index c6fe595c2..31ac1a2ec 100644
--- a/deb/remote.go
+++ b/deb/remote.go
@@ -847,11 +847,16 @@ func (collection *RemoteRepoCollection) Add(repo *RemoteRepo) error {
 // Update stores updated information about repo in DB
 func (collection *RemoteRepoCollection) Update(repo *RemoteRepo) error {
 	batch := collection.db.CreateBatch()
-
 	_ = batch.Put(repo.Key(), repo.Encode())
+
 	if repo.packageRefs != nil {
 		_ = batch.Put(repo.RefKey(), repo.packageRefs.Encode())
+	} else {
+		// Delete RefKey if packageRefs is nil
+		// This prevents inconsistent state where RefKey exists but is corrupted
+		_ = batch.Delete(repo.RefKey())
 	}
+
 	return batch.Write()
 }
 
diff --git a/deb/snapshot.go b/deb/snapshot.go
index 74f8865db..b96f3b400 100644
--- a/deb/snapshot.go
+++ b/deb/snapshot.go
@@ -227,10 +227,14 @@ func (collection *SnapshotCollection) Add(snapshot *Snapshot) error {
 // Update stores updated information about snapshot in DB
 func (collection *SnapshotCollection) Update(snapshot *Snapshot) error {
 	batch := collection.db.CreateBatch()
-
 	_ = batch.Put(snapshot.Key(), snapshot.Encode())
+
 	if snapshot.packageRefs != nil {
 		_ = batch.Put(snapshot.RefKey(), snapshot.packageRefs.Encode())
+	} else {
+		// Delete RefKey if packageRefs is nil
+		// This prevents inconsistent state where RefKey exists but is corrupted
+		_ = batch.Delete(snapshot.RefKey())
 	}
 
 	return batch.Write()