diff --git a/graphify/skill-copilot.md b/graphify/skill-copilot.md
index cfccee543..a18d8276b 100644
--- a/graphify/skill-copilot.md
+++ b/graphify/skill-copilot.md
@@ -823,6 +823,14 @@ if deleted:
 # Merge: new nodes/edges into existing graph
 G_existing.update(G_new)
 print(f'Merged: {G_existing.number_of_nodes()} nodes, {G_existing.number_of_edges()} edges')
+
+# Save manifest with the CURRENT full file list so the next --update
+# diffs against today's filesystem state, not the prior --update's
+# baseline. Without this, deleted files get reported as ghosts again
+# on every subsequent --update until a full rebuild runs.
+from graphify.detect import save_manifest
+save_manifest(incremental['files'])
+print('[graphify update] Manifest saved.')
 " 
 ```
 
diff --git a/graphify/skill.md b/graphify/skill.md
index 60d242209..10b2a56cc 100644
--- a/graphify/skill.md
+++ b/graphify/skill.md
@@ -931,6 +931,14 @@ merged_out = {
 }
 Path('graphify-out/.graphify_extract.json').write_text(json.dumps(merged_out))
 print(f'[graphify update] Merged extraction written ({len(merged_out[\"nodes\"])} nodes, {len(merged_out[\"edges\"])} edges)')
+
+# Save manifest with the CURRENT full file list so the next --update
+# diffs against today's filesystem state, not the prior --update's
+# baseline. Without this, deleted files get reported as ghosts again
+# on every subsequent --update until a full rebuild runs.
+from graphify.detect import save_manifest
+save_manifest(incremental['files'])
+print('[graphify update] Manifest saved.')
 " 
 ```