diff --git a/navi/overlay/apply.py b/navi/overlay/apply.py
index 65792ac..f4a93a3 100644
--- a/navi/overlay/apply.py
+++ b/navi/overlay/apply.py
@@ -189,6 +189,21 @@
 # ── live refresh ────────────────────────────────────────────────────────────
 
 
+def _staged_sections(previous: dict, merged: dict) -> list[str]:
+    """Sections that changed but only take effect at the next start.
+
+    ``llm`` and ``mcp_servers`` are consumed while the container is built —
+    backends and the MCP pool do not survive a swap — so a refresh that
+    changes them must say "restart", not quietly report the document applied.
+    ``profiles`` are rebuilt live and settings are diffed separately.
+    """
+    staged = []
+    for section in ("llm", "mcp_servers"):
+        if (previous.get(section) or {}) != (merged.get(section) or {}):
+            staged.append(section)
+    return staged
+
+
 def _ack(base_settings, fetched: Fetched, status: str, restart_required: list[str],
          errors: list[str]) -> None:
     if not base_settings.hive_url:
@@ -276,6 +291,7 @@
         # were handed back to local values, so it must run before we replace
         # ``state.merged``.
         hot, restart = apply_settings_live(validation.merged.get("settings") or {})
+        restart += _staged_sections(state.merged or {}, validation.merged)
         state.merged = validation.merged
         apply_profiles_registry_from_state()
 
diff --git a/tests/unit/overlay/test_apply.py b/tests/unit/overlay/test_apply.py
index 9c4094d..deb2727 100644
--- a/tests/unit/overlay/test_apply.py
+++ b/tests/unit/overlay/test_apply.py
@@ -252,6 +252,40 @@
     assert state.last_error is None
 
 
+def test_an_llm_change_is_staged_not_claimed_applied(state, monkeypatch):
+    monkeypatch.setattr(
+        apply_mod,
+        "fetch_layers",
+        lambda b: Fetched(
+            version=2,
+            layers=[{"name": "g", "config": {"llm": {"probe": {"interval_sec": 30}}}}],
+            hash="sha256:llm",
+        ),
+    )
+    result = refresh("test")
+    assert result["status"] == "staged"
+    assert "llm" in result["restart_required"]
+    # The document is remembered, so a later start picks it up from the cache.
+    assert state.merged["llm"]["probe"]["interval_sec"] == 30
+
+
+def test_a_settings_only_refresh_does_not_stage_llm(state, monkeypatch):
+    monkeypatch.setattr(
+        apply_mod,
+        "fetch_layers",
+        lambda b: Fetched(
+            version=3,
+            layers=[
+                {"name": "g", "config": {"settings": {"llm_complete_timeout": 42}}}
+            ],
+            hash="sha256:s",
+        ),
+    )
+    result = refresh("test")
+    assert "llm" not in result["restart_required"]
+    assert "mcp_servers" not in result["restart_required"]
+
+
 def test_refresh_staged_when_a_restart_is_needed(state, monkeypatch):
     monkeypatch.setattr(
         apply_mod,