diff --git a/packages/core/api/index.js b/packages/core/api/index.js
index 1a019c95b..f738b42e0 100644
--- a/packages/core/api/index.js
+++ b/packages/core/api/index.js
@@ -96,8 +96,6 @@ class Database {
     await this.migrations.migrate();
 
     this.monographs.init();
-
-    await this.syncer.cleanup();
   }
 
   async connectSSE() {
@@ -114,7 +112,8 @@ class Database {
       headers: { Authorization: `Bearer ${token}` },
     });
 
-    this.evtSource.onopen = function () {
+    this.evtSource.onopen = async () => {
+      await this.syncer.cleanup();
       console.log("SSE: opened channel successfully!");
     };
 
diff --git a/packages/core/api/sync/index.js b/packages/core/api/sync/index.js
index 53d4ba8fd..9b267e57a 100644
--- a/packages/core/api/sync/index.js
+++ b/packages/core/api/sync/index.js
@@ -145,6 +145,8 @@ export default class Sync {
         { collection: "content", ids: contentIds },
         token
       );
-    } catch (e) {}
+    } catch (e) {
+      console.error(e);
+    }
   }
 }
diff --git a/packages/core/collections/content.js b/packages/core/collections/content.js
index 6698e16a3..4be7986e0 100644
--- a/packages/core/collections/content.js
+++ b/packages/core/collections/content.js
@@ -57,14 +57,18 @@ export default class Content extends Collection {
   }
 
   async cleanup() {
-    const allContent = await this.all();
+    const indices = this._collection.indexer.indices;
+    await this._db.notes.init();
+    const notes = this._db.notes._collection.getRaw();
     let ids = [];
-    for (let content of allContent) {
-      const { noteId } = content;
-      const note = this._db.notes._collection.getItem(noteId);
-      if (!note || note.contentId !== content.id) {
-        ids.push(content.id);
-        await this._collection.deleteItem(content.id);
+    for (let contentId of indices) {
+      const noteIndex = notes.findIndex((note) => note.contentId === contentId);
+      const isOrphaned = noteIndex === -1;
+      if (isOrphaned) {
+        ids.push(contentId);
+        await this._collection.deleteItem(contentId);
+      } else if (notes[noteIndex].localOnly) {
+        ids.push(contentId);
       }
     }
     return ids;