diff --git a/docs/agent-lifecycle/config-changes.md b/docs/agent-lifecycle/config-changes.md
index fc058d19..cd5862d4 100644
--- a/docs/agent-lifecycle/config-changes.md
+++ b/docs/agent-lifecycle/config-changes.md
@@ -144,9 +144,11 @@ autoupdate flake-rev bump (one shot before per-agent rebuilds).
 carries `hyperhive_flake`, `dashboard_port`, and the rest of the
 per-hive config — is the idempotent reconciler called by `provision_container`,
 `destroy`, `rebuild`, and the startup migration. Renders `flake.nix`
-from the agent list; if it differs from disk, runs
+from the agent list; if it differs from disk, or `flake.nix` or `flake.lock`
+has an uncommitted change (a sync stopped before its commit), runs
 `nix flake lock` + commits as `regenerate meta flake` (or
-`seed meta from N agent(s)` on the first call).
+`seed meta from N agent(s)` on the first call). A clean tree whose
+`flake.nix` already matches returns without running nix.
 
 The root agent has `/meta` RO-bound inside its container:
 `git -C /meta log --oneline` is the swarm-wide deploy log,
diff --git a/hive-c0re/src/meta.rs b/hive-c0re/src/meta.rs
index 4333a208..715886b6 100644
--- a/hive-c0re/src/meta.rs
+++ b/hive-c0re/src/meta.rs
@@ -148,11 +148,22 @@ async fn stage_generated_meta_files(dir: &std::path::Path) -> Result<()> {
     Ok(())
 }
 
+/// Meta files `sync_agents` writes and locks; an uncommitted change to them
+/// means an earlier sync stopped before its commit.
+const SYNC_OWNED_PATHS: &[&str] = &["flake.nix", "flake.lock"];
+
+/// Whether `sync_agents` has nothing to do: the repo exists, the rendered
+/// flake equals the one on disk, and no sync-owned file is uncommitted.
+fn can_skip_sync(initial: bool, flake_unchanged: bool, uncommitted: bool) -> bool {
+    !initial && flake_unchanged && !uncommitted
+}
+
 /// Idempotently reconcile the meta repo with the current agent set.
 /// First call inits the git repo, runs `nix flake lock`, and lands a
 /// seed commit. Subsequent calls only touch `flake.nix` when the
 /// rendered contents differ from disk; an unchanged `flake.nix` is a
-/// no-op.
+/// no-op unless `flake.nix` or `flake.lock` is uncommitted, in which case
+/// the lock and commit run again.
 pub async fn sync_agents(hive: &HiveEnv, agents: &[AgentSpec]) -> Result<()> {
     let _guard = lock_meta("sync_agents").await;
     // Before anything is written: a hive without a forge URL would deploy a
@@ -174,9 +185,18 @@ pub async fn sync_agents(hive: &HiveEnv, agents: &[AgentSpec]) -> Result<()> {
     let on_disk = std::fs::read_to_string(&flake_path).unwrap_or_default();
     let initial = !dir.join(".git").exists();
 
-    if !initial && on_disk == new_flake {
+    let flake_unchanged = on_disk == new_flake;
+    let uncommitted = if !initial && flake_unchanged {
+        paths_dirty(&dir, SYNC_OWNED_PATHS).await?
+    } else {
+        false
+    };
+    if can_skip_sync(initial, flake_unchanged, uncommitted) {
         return Ok(());
     }
+    if uncommitted {
+        tracing::info!("sync_agents: resuming an uncommitted flake.nix/flake.lock change");
+    }
 
     // Safety guard: refuse to write an empty agent list over a non-empty
     // on-disk flake. An empty `agents` slice is never intentional — it
@@ -1162,6 +1182,48 @@ async fn nix(dir: &Path, args: &[&str]) -> Result<()> {
 mod tests {
     use super::*;
 
+    #[test]
+    fn sync_skips_only_when_clean_unchanged_and_not_initial() {
+        assert!(can_skip_sync(false, true, false));
+        assert!(!can_skip_sync(false, true, true), "interrupted sync");
+        assert!(!can_skip_sync(false, false, false), "flake changed");
+        assert!(!can_skip_sync(true, true, false), "no repo yet");
+    }
+
+    /// An interrupted sync leaves the new `flake.nix` written with the old
+    /// lock; the dirty check over the sync-owned paths must see it, and stay
+    /// quiet on a clean tree and on files sync does not own.
+    #[tokio::test]
+    async fn interrupted_sync_leaves_sync_owned_paths_dirty() {
+        let tmp = tempfile::tempdir().expect("tempdir");
+        let dir = tmp.path();
+        git(dir, &["init", "--initial-branch=main"])
+            .await
+            .expect("git init");
+        std::fs::write(dir.join("flake.nix"), "old").expect("write");
+        std::fs::write(dir.join("flake.lock"), "lock-old").expect("write");
+        std::fs::write(dir.join("other.json"), "{}").expect("write");
+        git(dir, &["add", "-A"]).await.expect("add");
+        git_commit(dir, "seed").await.expect("seed commit");
+        assert!(!paths_dirty(dir, SYNC_OWNED_PATHS).await.expect("check"));
+
+        std::fs::write(dir.join("other.json"), r#"{"x":1}"#).expect("write");
+        assert!(
+            !paths_dirty(dir, SYNC_OWNED_PATHS).await.expect("check"),
+            "a file sync does not own is not an interrupted sync"
+        );
+
+        std::fs::write(dir.join("flake.nix"), "new").expect("write");
+        git(dir, &["add", "flake.nix"]).await.expect("stage");
+        assert!(
+            paths_dirty(dir, SYNC_OWNED_PATHS).await.expect("check"),
+            "new flake.nix written but not committed"
+        );
+        git(dir, &["add", "-A"]).await.expect("add");
+        git_commit(dir, "resume").await.expect("commit");
+        assert!(!paths_dirty(dir, SYNC_OWNED_PATHS).await.expect("check"));
+    }
+
     /// A path-limited commit must leave an unrelated staged file untouched.
     #[tokio::test]
     async fn path_limited_commit_leaves_unrelated_staged_file_alone() {