diff --git a/packages/backend/server/src/models/copilot-workspace.ts b/packages/backend/server/src/models/copilot-workspace.ts
index c250d1f65..eab737d52 100644
--- a/packages/backend/server/src/models/copilot-workspace.ts
+++ b/packages/backend/server/src/models/copilot-workspace.ts
@@ -152,21 +152,57 @@ export class CopilotWorkspaceConfigModel extends BaseModel {
     return docIds.filter(id => ignored.has(id));
   }
 
+  // check if a docId has only placeholder embeddings
+  @Transactional()
+  async hasPlaceholder(workspaceId: string, docId: string): Promise<boolean> {
+    const [total, nonPlaceholder] = await Promise.all([
+      this.db.aiWorkspaceEmbedding.count({ where: { workspaceId, docId } }),
+      this.db.aiWorkspaceEmbedding.count({
+        where: {
+          workspaceId,
+          docId,
+          NOT: { AND: [{ chunk: 0 }, { content: '' }] },
+        },
+      }),
+    ]);
+    return total > 0 && nonPlaceholder === 0;
+  }
+
+  private getEmbeddableCondition(
+    workspaceId: string,
+    ignoredDocIds?: string[]
+  ): Prisma.SnapshotWhereInput {
+    const condition: Prisma.SnapshotWhereInput['AND'] = [
+      { id: { not: workspaceId } },
+      { id: { not: { contains: '$' } } },
+      { id: { not: { contains: ':settings:' } } },
+      { blob: { not: new Uint8Array([0, 0]) } },
+    ];
+    if (ignoredDocIds && ignoredDocIds.length > 0) {
+      condition.push({ id: { notIn: ignoredDocIds } });
+    }
+    return { workspaceId, AND: condition };
+  }
+
+  @Transactional()
+  async listEmbeddableDocIds(workspaceId: string) {
+    const condition = this.getEmbeddableCondition(workspaceId);
+    const rows = await this.db.snapshot.findMany({
+      where: condition,
+      select: { id: true },
+    });
+    return rows.map(r => r.id);
+  }
+
   @Transactional()
   async getEmbeddingStatus(workspaceId: string) {
     const ignoredDocIds = (await this.listIgnoredDocIds(workspaceId)).map(
       d => d.docId
     );
-    const snapshotCondition = {
+    const snapshotCondition = this.getEmbeddableCondition(
       workspaceId,
-      AND: [
-        { id: { notIn: ignoredDocIds } },
-        { id: { not: workspaceId } },
-        { id: { not: { contains: '$' } } },
-        { id: { not: { contains: ':settings:' } } },
-        { blob: { not: new Uint8Array([0, 0]) } },
-      ],
-    };
+      ignoredDocIds
+    );
 
     const [docTotal, docEmbedded, fileTotal, fileEmbedded] = await Promise.all([
       this.db.snapshot.findMany({
diff --git a/packages/backend/server/src/plugins/copilot/embedding/job.ts b/packages/backend/server/src/plugins/copilot/embedding/job.ts
index 303ec2600..6f2db734b 100644
--- a/packages/backend/server/src/plugins/copilot/embedding/job.ts
+++ b/packages/backend/server/src/plugins/copilot/embedding/job.ts
@@ -532,11 +532,14 @@ export class CopilotEmbeddingJob {
       return;
     }
 
-    const docIdsInEmbedding =
-      await this.models.copilotContext.listWorkspaceDocEmbedding(workspaceId);
-    if (!docIdsInEmbedding.length) {
+    const [docIdsInEmbedding, docIdsInSnapshots] = await Promise.all([
+      this.models.copilotContext.listWorkspaceDocEmbedding(workspaceId),
+      this.models.copilotWorkspace.listEmbeddableDocIds(workspaceId),
+    ]);
+
+    if (!docIdsInEmbedding.length && !docIdsInSnapshots.length) {
       this.logger.verbose(
-        `No doc embeddings found in workspace ${workspaceId}, skipping cleanup`
+        `No doc embeddings and snapshots found in workspace ${workspaceId}, skipping cleanup`
       );
       await this.models.workspace.update(
         workspaceId,
@@ -549,10 +552,17 @@ export class CopilotEmbeddingJob {
     const docIdsInWorkspace = readAllDocIdsFromWorkspaceSnapshot(snapshot.blob);
     const docIdsInWorkspaceSet = new Set(docIdsInWorkspace);
 
-    const deletedDocIds = docIdsInEmbedding.filter(
-      docId => !docIdsInWorkspaceSet.has(docId)
+    const deletedDocIds = new Set(
+      [...docIdsInEmbedding, ...docIdsInSnapshots].filter(
+        docId => !docIdsInWorkspaceSet.has(docId)
+      )
     );
     for (const docId of deletedDocIds) {
+      const isPlaceholder = await this.models.copilotWorkspace.hasPlaceholder(
+        workspaceId,
+        docId
+      );
+      if (isPlaceholder) continue;
       await this.models.copilotContext.deleteWorkspaceEmbedding(
         workspaceId,
         docId