From 4c54e640e0af8766f400d95be71eb9a0b9a4ce3f Mon Sep 17 00:00:00 2001
From: Georgi Gardev <georgi@gar.dev>
Date: Sun, 11 Jan 2026 22:11:39 +0200
Subject: [PATCH] fix: annotations marked as deleted (fixes #86)

---
 .../server/src/annotations/annotations-repository.ts | 11 ++++++++++-
 apps/server/src/upload/upload-service.ts             | 12 +++---------
 package.json                                         |  3 ++-
 3 files changed, 15 insertions(+), 11 deletions(-)

diff --git a/apps/server/src/annotations/annotations-repository.ts b/apps/server/src/annotations/annotations-repository.ts
index 27c7430..39cbe3d 100644
--- a/apps/server/src/annotations/annotations-repository.ts
+++ b/apps/server/src/annotations/annotations-repository.ts
@@ -75,7 +75,16 @@ export class AnnotationsRepository {
           .onConflict(['book_md5', 'device_id', 'page_ref', 'datetime'])
           // Only update fields that users can actually change in KoReader
           // Do NOT update pageno/total_pages - these are historical context!
-          .merge(['text', 'note', 'datetime_updated', 'chapter', 'updated_at', 'drawer', 'color']);
+          .merge([
+            'text',
+            'note',
+            'datetime_updated',
+            'chapter',
+            'updated_at',
+            'drawer',
+            'color',
+            'deleted_at',
+          ]);
       }
     };
 
diff --git a/apps/server/src/upload/upload-service.ts b/apps/server/src/upload/upload-service.ts
index a2ca418..ec9c168 100644
--- a/apps/server/src/upload/upload-service.ts
+++ b/apps/server/src/upload/upload-service.ts
@@ -123,16 +123,10 @@ export class UploadService {
           )
         );
 
-        const bookMd5s = newBooks.map((b) => b.md5).filter((md5): md5 is string => !!md5);
-
+        // FIXME: with this, if there is only 1 annotation and it gets removed, it won't get marked as deleted, because `annotationsByBook` will be empty. It will only get marked as deleted if the user adds another annotation to trigger an update on the book.
         await Promise.all(
-          bookMd5s.map((bookMd5) =>
-            this.detectAndMarkDeletedAnnotations(
-              bookMd5,
-              deviceId,
-              annotationsByBook[bookMd5] || [],
-              trx
-            )
+          Object.entries(annotationsByBook).map(([bookMd5, annotations]) =>
+            this.detectAndMarkDeletedAnnotations(bookMd5, deviceId, annotations, trx)
           )
         );
       }
diff --git a/package.json b/package.json
index b43509c..65975d7 100644
--- a/package.json
+++ b/package.json
@@ -13,7 +13,8 @@
   ],
   "scripts": {
     "build": "turbo run build",
-    "test:coverage": "turbo run test:coverage"
+    "test:coverage": "turbo run test:coverage",
+    "dev": "turbo run dev --parallel"
   },
   "devDependencies": {
     "prettier": "3.6.2",