diff --git a/server/src/agents/pool/pipeline/advance/mod.rs b/server/src/agents/pool/pipeline/advance/mod.rs
index 0368fccf..7f97cd42 100644
--- a/server/src/agents/pool/pipeline/advance/mod.rs
+++ b/server/src/agents/pool/pipeline/advance/mod.rs
@@ -414,6 +414,7 @@ impl AgentPool {
                             slog_error!("[pipeline] Failed to move '{story_id}' to done: {e}");
                         }
                         self.remove_agents_for_story(story_id);
+                        crate::crdt_state::delete_merge_job(story_id);
                         // TODO: Re-enable worktree cleanup once we have persistent agent logs.
                         // Removing worktrees destroys evidence needed to debug empty-commit agents.
                         // let config =