diff --git a/hermes_cli/cli_info_mixin.py b/hermes_cli/cli_info_mixin.py
index 936bbcb6b9..76aa226a70 100644
--- a/hermes_cli/cli_info_mixin.py
+++ b/hermes_cli/cli_info_mixin.py
@@ -16,7 +16,7 @@ import time
 
 from hermes_constants import is_termux as _is_termux_environment
 from rich.markup import escape as _escape
-from utils import base_url_hostname
+from utils import base_url_hostname, file_signature
 
 from hermes_cli.cli_modal_mixin import _gated_confirm
 from hermes_cli.colors import Colors as _Colors
@@ -818,13 +818,13 @@ class CLIInfoMixin:
         if not cfg_path.exists():
             return
         try:
-            mtime = cfg_path.stat().st_mtime
+            sig = file_signature(cfg_path.stat())
         except OSError:
             return
-        if mtime == self._config_mtime:
+        if sig == self._config_sig:
             return  # unchanged — fast path
 
-        self._config_mtime = mtime
+        self._config_sig = sig
         try:
             with open(cfg_path, encoding="utf-8") as f:
                 new_cfg = _yaml.safe_load(f) or {}
diff --git a/hermes_cli/cli_tui_mixin.py b/hermes_cli/cli_tui_mixin.py
index 77d9e99534..9562a9eafb 100644
--- a/hermes_cli/cli_tui_mixin.py
+++ b/hermes_cli/cli_tui_mixin.py
@@ -1819,7 +1819,7 @@ class CLITuiMixin:
         # Config file watcher — detect mcp_servers changes and auto-reload.
         from hermes_cli.config import get_config_path as _get_config_path
         _cfg_path = _get_config_path()
-        self._config_mtime: float = _cfg_path.stat().st_mtime if _cfg_path.exists() else 0.0
+        self._config_sig: tuple | None = file_signature(_cfg_path.stat()) if _cfg_path.exists() else None
         self._config_mcp_servers: dict = self.config.get("mcp_servers") or {}
         self._last_config_check: float = 0.0  # monotonic time of last check
 
diff --git a/hermes_cli/config.py b/hermes_cli/config.py
index b72bf8d8e1..e46f602e4d 100644
--- a/hermes_cli/config.py
+++ b/hermes_cli/config.py
@@ -204,7 +204,7 @@ _LAST_EXPANDED_CONFIG_BY_PATH: Dict[str, Any] = {}
 # atomic_yaml_write which produces a fresh inode, so stat() sees a new signature and the next load
 # repopulates automatically — no explicit invalidation hook. See #58514.
 _LOAD_CONFIG_CACHE: Dict[str, Tuple[int, ...]] = {}
-# path -> (mtime_ns, size, raw yaml dict) for read_raw_config() (no defaults merged in).
+# path -> (mtime_ns, size, ino, ctime_ns, raw yaml dict) for read_raw_config() (no defaults merged in).
 _RAW_CONFIG_CACHE: Dict[str, Tuple[int, ...]] = {}
 
 # Env var names written to .env that aren't in OPTIONAL_ENV_VARS (managed by setup/provider
@@ -2392,7 +2392,7 @@ def save_config(
 
 # load_env() memo keyed on (path, *file_signature). Editing .env bumps mtime/inode -> rebuild;
 # invalidate_env_cache() is the explicit knob for writers on coarse-mtime filesystems.
-_env_cache: Optional[Tuple[Tuple[str, Optional[float], Optional[int]], Dict[str, str]]] = None
+_env_cache: Optional[Tuple[Tuple[str, Optional[Tuple[int, int, int, int]]], Dict[str, str]]] = None
 
 
 def load_env() -> Dict[str, str]:
diff --git a/model_tools.py b/model_tools.py
index 7f26e94fc3..f0e56c19e2 100644
--- a/model_tools.py
+++ b/model_tools.py
@@ -22,6 +22,7 @@ from tools.registry import CHECK_FN_CACHE_BYPASS, check_fn_cache_scope, discover
 from tools.registry import _MAX_TOOL_ERROR_CHARS as _TOOL_ERROR_MAX_LEN
 from toolsets import resolve_toolset, validate_toolset
 from tools.arg_coercion import coerce_tool_args
+from utils import file_signature
 
 logger = logging.getLogger(__name__)
 
@@ -257,7 +258,7 @@ def _tool_defs_cache_key(
     """Memo key for get_tool_definitions, or None when caching must be bypassed.
 
     Covers every argument plus everything that changes the result without one:
-    registry generation, config.yaml mtime/size (dynamic schemas), kanban
+    registry generation, config.yaml stat signature (dynamic schemas), kanban
     context, profile scope. check_fn results are TTL-cached in the registry.
     """
     profile_scope = check_fn_cache_scope()
@@ -266,7 +267,7 @@ def _tool_defs_cache_key(
     try:
         from hermes_cli.config import get_config_path
         cfg_stat = get_config_path().stat()
-        cfg_fp = (cfg_stat.st_mtime_ns, cfg_stat.st_size)
+        cfg_fp = file_signature(cfg_stat)
     except (FileNotFoundError, OSError, ImportError):
         cfg_fp = None
     return (
diff --git a/tests/conftest.py b/tests/conftest.py
index 0fd5ef8e69..7cbabca510 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -920,7 +920,7 @@ def _reset_tui_gateway_server_state():
     if mod is not None:
         snapshot = {
             "methods": dict(mod._methods),
-            "cfg": (mod._cfg_cache, mod._cfg_mtime, mod._cfg_path),
+            "cfg": (mod._cfg_cache, mod._cfg_sig, mod._cfg_path),
             "db": (mod._db, mod._db_error),
             "real_stdout": mod._real_stdout,
         }
@@ -951,7 +951,7 @@ def _reset_tui_gateway_server_state():
     if snapshot is not None:
         mod._methods.clear()
         mod._methods.update(snapshot["methods"])
-        mod._cfg_cache, mod._cfg_mtime, mod._cfg_path = snapshot["cfg"]
+        mod._cfg_cache, mod._cfg_sig, mod._cfg_path = snapshot["cfg"]
         mod._db, mod._db_error = snapshot["db"]
         mod._real_stdout = snapshot["real_stdout"]
     else:
@@ -959,7 +959,7 @@ def _reset_tui_gateway_server_state():
         # for the globals we could not snapshot (``_methods`` is left to
         # the importing file's fixture, see block comment above).
         mod._cfg_cache = None
-        mod._cfg_mtime = None
+        mod._cfg_sig = None
         mod._cfg_path = None
         mod._db = None
         mod._db_error = None
diff --git a/tests/hermes_cli/test_cli_mcp_config_watch.py b/tests/hermes_cli/test_cli_mcp_config_watch.py
index acfc7a3473..0f033518b4 100644
--- a/tests/hermes_cli/test_cli_mcp_config_watch.py
+++ b/tests/hermes_cli/test_cli_mcp_config_watch.py
@@ -3,6 +3,8 @@ import time
 from pathlib import Path
 from unittest.mock import MagicMock, patch
 
+from utils import file_signature
+
 
 def _make_cli(tmp_path, mcp_servers=None, extra_config=None):
     """Create a minimal HermesCLI instance with mocked config."""
@@ -18,7 +20,7 @@ def _make_cli(tmp_path, mcp_servers=None, extra_config=None):
 
     cfg_file = tmp_path / "config.yaml"
     cfg_file.write_text("mcp_servers: {}\n")
-    obj._config_mtime = cfg_file.stat().st_mtime
+    obj._config_sig = file_signature(cfg_file.stat())
 
     obj._reload_mcp = MagicMock()
     obj._busy_command = MagicMock()
@@ -40,7 +42,7 @@ class TestMCPConfigWatch:
 
         # Simulate user adding a new MCP server to config.yaml
         cfg_file.write_text(yaml.dump({"mcp_servers": {"github": {"url": "https://mcp.github.com"}}}))
-        obj._config_mtime = 0.0  # force stale mtime
+        obj._config_sig = None  # force stale mtime
 
         with patch("hermes_cli.config.get_config_path", return_value=cfg_file):
             obj._check_config_mcp_changes()
@@ -54,7 +56,7 @@ class TestMCPConfigWatch:
 
         # Simulate user removing the server
         cfg_file.write_text(yaml.dump({"mcp_servers": {}}))
-        obj._config_mtime = 0.0
+        obj._config_sig = None
 
         with patch("hermes_cli.config.get_config_path", return_value=cfg_file):
             obj._check_config_mcp_changes()
@@ -87,7 +89,7 @@ class TestMCPConfigWatch:
             "mcp": {"auto_reload_on_config_change": False},
             "mcp_servers": {"github": {"url": "https://mcp.github.com"}},
         }))
-        obj._config_mtime = 0.0  # force stale mtime
+        obj._config_sig = None  # force stale mtime
 
         with patch("hermes_cli.config.get_config_path", return_value=cfg_file):
             obj._check_config_mcp_changes()
@@ -110,13 +112,13 @@ class TestMCPConfigWatch:
             "mcp": {"auto_reload_on_config_change": False},
             "mcp_servers": {"github": {"url": "https://mcp.github.com"}},
         }))
-        obj._config_mtime = 0.0
+        obj._config_sig = None
 
         with patch("hermes_cli.config.get_config_path", return_value=cfg_file):
             obj._check_config_mcp_changes()
             # Second pass: same file content, new mtime — no reload, no change.
             obj._last_config_check = 0.0
-            obj._config_mtime = 0.0
+            obj._config_sig = None
             obj._check_config_mcp_changes()
 
         obj._reload_mcp.assert_not_called()
@@ -139,7 +141,7 @@ class TestMCPConfigWatch:
             "auxiliary": {"mcp": {"auto_reload_on_config_change": False}},
             "mcp_servers": {"github": {"url": "https://mcp.github.com"}},
         }))
-        obj._config_mtime = 0.0
+        obj._config_sig = None
 
         with patch("hermes_cli.config.get_config_path", return_value=cfg_file):
             obj._check_config_mcp_changes()
@@ -184,10 +186,30 @@ class TestMCPConfigWatch:
             "agent": {"reasoning_effort": "high"},
             "mcp_servers": raw_servers,
         }))
-        obj._config_mtime = 0.0
+        obj._config_sig = None
 
         with patch("hermes_cli.config.get_config_path", return_value=cfg_file):
             obj._check_config_mcp_changes()
 
         obj._reload_mcp.assert_not_called()
         assert "MCP server config changed" not in capsys.readouterr().out
+
+
+def test_pinned_mtime_same_size_replacement_triggers_reload(tmp_path):
+    """#111105: cp -p / rsync -t style replacement (same mtime, same size) must still reload."""
+    import os
+    import shutil
+
+    obj, cfg_file = _make_cli(tmp_path, mcp_servers={"bb": {"command": "b"}})
+    cfg_file.write_text("mcp_servers:\n  bb: {command: b}\n")
+    obj._config_sig = file_signature(cfg_file.stat())
+    other = tmp_path / "other.yaml"
+    other.write_text("mcp_servers:\n  aa: {command: a}\n")
+    shutil.copy2(other, cfg_file)
+    os.utime(cfg_file, ns=(obj._config_sig[0], obj._config_sig[0]))
+
+    with patch("hermes_cli.config.get_config_path", return_value=cfg_file):
+        obj._check_config_mcp_changes()
+
+    obj._reload_mcp.assert_called_once()
+    assert obj._config_mcp_servers == {"aa": {"command": "a"}}
diff --git a/tests/tools/test_mcp_stability.py b/tests/tools/test_mcp_stability.py
index 974ad09cb5..9ce5cf979c 100644
--- a/tests/tools/test_mcp_stability.py
+++ b/tests/tools/test_mcp_stability.py
@@ -443,7 +443,7 @@ class TestMCPReloadTimeout:
 
         # Create a mock HermesCLI-like object with the needed attributes
         class FakeCLI:
-            _config_mtime = 0.0
+            _config_sig = None
             _config_mcp_servers = {}
             _last_config_check = 0.0
             _command_running = False
diff --git a/tests/tools/test_model_tools.py b/tests/tools/test_model_tools.py
index 0d93357679..2e02e83874 100644
--- a/tests/tools/test_model_tools.py
+++ b/tests/tools/test_model_tools.py
@@ -570,7 +570,9 @@ class TestBridgeDispatch:
         assert disp.call_args.args[0] == "mcp_x" and disp.call_args.args[1] == {"a": 1}
 
 
-# =========================================================================
+# ==================================================================
+
+
 # Browser schema retrieval hints
 # =========================================================================
 
@@ -600,3 +602,22 @@ class TestBrowserRetrievalHints:
         rendered = " ".join(d["function"]["description"] for d in _apply_dynamic_schemas(defs + self._defs("terminal")))
         assert "web_search" not in rendered
         assert "web_extract" not in rendered
+
+
+def test_tool_defs_cache_key_sees_config_replacement_with_pinned_mtime(tmp_path):
+    """#111105: a same-size config.yaml swapped in with the old mtime must change the memo key."""
+    import os
+    import shutil
+
+    from model_tools import _tool_defs_cache_key
+
+    cfg = tmp_path / "config.yaml"
+    cfg.write_text("mcp_servers:\n  aa: {command: a}\n", encoding="utf-8")
+    with patch("hermes_cli.config.get_config_path", return_value=cfg):
+        before = _tool_defs_cache_key(None, None, False)
+        st = cfg.stat()
+        other = tmp_path / "other.yaml"
+        other.write_text("mcp_servers:\n  bb: {command: b}\n", encoding="utf-8")
+        shutil.copy2(other, cfg)
+        os.utime(cfg, ns=(st.st_atime_ns, st.st_mtime_ns))
+        assert _tool_defs_cache_key(None, None, False) != before
diff --git a/tests/tui_gateway/test_config_profile_scope.py b/tests/tui_gateway/test_config_profile_scope.py
index d7d1a8e02e..f10e2d61cc 100644
--- a/tests/tui_gateway/test_config_profile_scope.py
+++ b/tests/tui_gateway/test_config_profile_scope.py
@@ -45,7 +45,7 @@ def _homes(tmp_path: Path) -> tuple[Path, Path]:
 
 def _reset_cfg_cache() -> None:
     server._cfg_cache = None
-    server._cfg_mtime = None
+    server._cfg_sig = None
     server._cfg_path = None
 
 
diff --git a/tests/tui_gateway/test_config_set_display_toggles.py b/tests/tui_gateway/test_config_set_display_toggles.py
index 2139314f26..ef1578e55d 100644
--- a/tests/tui_gateway/test_config_set_display_toggles.py
+++ b/tests/tui_gateway/test_config_set_display_toggles.py
@@ -16,9 +16,9 @@ from tui_gateway import server
 def config_home(tmp_path, monkeypatch):
     """Point the server's config read/write at a temp file."""
     monkeypatch.setattr(server, "_hermes_home", tmp_path)
-    server._cfg_cache = server._cfg_mtime = server._cfg_path = None
+    server._cfg_cache = server._cfg_sig = server._cfg_path = None
     yield tmp_path / "config.yaml"
-    server._cfg_cache = server._cfg_mtime = server._cfg_path = None
+    server._cfg_cache = server._cfg_sig = server._cfg_path = None
 
 
 def _set(key, value):
diff --git a/tests/tui_gateway/test_config_set_voice_chat_mode.py b/tests/tui_gateway/test_config_set_voice_chat_mode.py
index 5dee8097db..35b08c2844 100644
--- a/tests/tui_gateway/test_config_set_voice_chat_mode.py
+++ b/tests/tui_gateway/test_config_set_voice_chat_mode.py
@@ -14,9 +14,9 @@ from tui_gateway import server
 @pytest.fixture
 def config_home(tmp_path, monkeypatch):
     monkeypatch.setattr(server, "_hermes_home", tmp_path)
-    server._cfg_cache = server._cfg_mtime = server._cfg_path = None
+    server._cfg_cache = server._cfg_sig = server._cfg_path = None
     yield tmp_path / "config.yaml"
-    server._cfg_cache = server._cfg_mtime = server._cfg_path = None
+    server._cfg_cache = server._cfg_sig = server._cfg_path = None
 
 
 def _set(value):
diff --git a/tests/tui_gateway/test_goal_command.py b/tests/tui_gateway/test_goal_command.py
index 674ca15f36..c767d61ed0 100644
--- a/tests/tui_gateway/test_goal_command.py
+++ b/tests/tui_gateway/test_goal_command.py
@@ -60,7 +60,7 @@ def server(hermes_home, monkeypatch):
     # originals on teardown so nothing leaks to later tests either.
     monkeypatch.setattr(mod, "_hermes_home", hermes_home)
     monkeypatch.setattr(mod, "_cfg_cache", None)
-    monkeypatch.setattr(mod, "_cfg_mtime", None)
+    monkeypatch.setattr(mod, "_cfg_sig", None)
     monkeypatch.setattr(mod, "_cfg_path", None)
     yield mod
     # Reset module-level session state without re-importing. importlib.reload
diff --git a/tests/tui_gateway/test_protocol.py b/tests/tui_gateway/test_protocol.py
index 9ba50ac3fc..601872d5dd 100644
--- a/tests/tui_gateway/test_protocol.py
+++ b/tests/tui_gateway/test_protocol.py
@@ -1357,7 +1357,7 @@ def test_skin_live_switch_end_to_end(server, tmp_path, monkeypatch):
     monkeypatch.setattr(skin_engine, "get_hermes_home", lambda: tmp_path)
     monkeypatch.setattr(server, "_hermes_home", tmp_path)
     monkeypatch.setattr(server, "_last_skin_sig", None, raising=False)
-    server._cfg_cache = server._cfg_mtime = server._cfg_path = None
+    server._cfg_cache = server._cfg_sig = server._cfg_path = None
 
     emitted = []
     monkeypatch.setattr(server, "_emit", lambda ev, sid, payload=None: emitted.append((ev, payload)))
diff --git a/tests/tui_gateway/test_session_control.py b/tests/tui_gateway/test_session_control.py
index 64e1f2f603..774243fceb 100644
--- a/tests/tui_gateway/test_session_control.py
+++ b/tests/tui_gateway/test_session_control.py
@@ -39,7 +39,7 @@ def server(hermes_home, monkeypatch):
         mod = importlib.import_module("tui_gateway.server")
     monkeypatch.setattr(mod, "_hermes_home", hermes_home)
     monkeypatch.setattr(mod, "_cfg_cache", None)
-    monkeypatch.setattr(mod, "_cfg_mtime", None)
+    monkeypatch.setattr(mod, "_cfg_sig", None)
     monkeypatch.setattr(mod, "_cfg_path", None)
     yield mod
     mod._sessions.clear()
diff --git a/tests/tui_gateway/test_tui_gateway_server.py b/tests/tui_gateway/test_tui_gateway_server.py
index 0a80e39b44..3361abb7b7 100644
--- a/tests/tui_gateway/test_tui_gateway_server.py
+++ b/tests/tui_gateway/test_tui_gateway_server.py
@@ -105,7 +105,7 @@ def test_session_slot_is_claimed_on_first_turn_not_on_create(monkeypatch, tmp_pa
 
     try:
         server._cfg_cache = None
-        server._cfg_mtime = None
+        server._cfg_sig = None
         server._cfg_path = None
         _clear_server_sessions()
         monkeypatch.setattr(server, "_start_agent_build", lambda *args, **kwargs: None)
@@ -139,7 +139,7 @@ def test_session_slot_is_claimed_on_first_turn_not_on_create(monkeypatch, tmp_pa
     finally:
         _clear_server_sessions()
         server._cfg_cache = None
-        server._cfg_mtime = None
+        server._cfg_sig = None
         server._cfg_path = None
         reset_hermes_home_override(token)
 
@@ -22496,3 +22496,23 @@ def test_workspace_move_rehomes_running_session(monkeypatch, tmp_path):
     assert captured["row_update"] == (target, str(new_cwd))
     assert live["cwd"] == str(new_cwd)
     assert live.get("explicit_cwd") is True
+
+
+def test_load_cfg_raw_sees_replacement_with_pinned_mtime_and_size(monkeypatch, tmp_path):
+    """#111105: the raw-config cache must not serve (and later write back) a stale document after a
+    same-size replacement that keeps the old mtime."""
+    import shutil
+
+    cfg = tmp_path / "config.yaml"
+    cfg.write_text("model:\n  default: bbbb-route\n", encoding="utf-8")
+    monkeypatch.setattr(server, "_active_config_path", lambda: cfg)
+    monkeypatch.setattr(server, "_cfg_cache", None)
+    monkeypatch.setattr(server, "_cfg_sig", None)
+    monkeypatch.setattr(server, "_cfg_path", None)
+    assert server._load_cfg_raw()["model"]["default"] == "bbbb-route"
+    st = cfg.stat()
+    other = tmp_path / "other.yaml"
+    other.write_text("model:\n  default: aaaa-route\n", encoding="utf-8")
+    shutil.copy2(other, cfg)
+    os.utime(cfg, ns=(st.st_atime_ns, st.st_mtime_ns))
+    assert server._load_cfg_raw()["model"]["default"] == "aaaa-route"
diff --git a/tui_gateway/server.py b/tui_gateway/server.py
index 0787278f1b..ebe1c1e721 100644
--- a/tui_gateway/server.py
+++ b/tui_gateway/server.py
@@ -26,7 +26,7 @@ from hermes_constants import (
     get_hermes_home, get_hermes_home_override, profile_name_for_home,
     reset_hermes_home_override, set_hermes_home_override)
 from hermes_cli.env_loader import load_hermes_dotenv
-from utils import is_truthy_value
+from utils import file_signature, is_truthy_value
 from hermes_state_ids import new_session_id
 from tools.environments.local import hermes_subprocess_env
 from agent.replay_cleanup import canonicalize_replay_history
@@ -96,7 +96,7 @@ _cfg_lock = threading.Lock()
 _profile_ui_meta_lock = threading.Lock()
 _sessions_lock = threading.RLock()  # reentrant: _close_session_by_id may run under callers that already hold it
 _cfg_cache: dict | None = None
-_cfg_mtime: float | None = None
+_cfg_sig: tuple | None = None
 _cfg_path = None
 _session_resume_lock = threading.Lock()
 _SLASH_WORKER_TIMEOUT_S = max(5.0, env_float("HERMES_TUI_SLASH_TIMEOUT_S", 45.0))
@@ -1227,17 +1227,17 @@ def _load_cfg_raw() -> dict:
     read→mutate→``_save_cfg`` round-trips and raw inspection (defaults / managed overlay / ``${VAR}``
     expansion applied here would be persisted on the next save). Behavioral reads use :func:`_load_cfg`.
     Cache keyed on the resolved path so profiles don't clobber."""
-    global _cfg_cache, _cfg_mtime, _cfg_path
+    global _cfg_cache, _cfg_sig, _cfg_path
     with contextlib.suppress(Exception):
         p = _active_config_path()
-        mtime = p.stat().st_mtime if p.exists() else None
+        sig = file_signature(p.stat()) if p.exists() else None
         with _cfg_lock:
-            if _cfg_cache is not None and _cfg_mtime == mtime and _cfg_path == p:
+            if _cfg_cache is not None and _cfg_sig == sig and _cfg_path == p:
                 return copy.deepcopy(_cfg_cache)
         from hermes_cli.config import read_user_config_raw
         data = read_user_config_raw(p) if p.exists() else {}
         with _cfg_lock:  # cache the RAW config: _save_cfg writes _cfg_cache back to disk
-            _cfg_cache, _cfg_mtime, _cfg_path = copy.deepcopy(data), mtime, p
+            _cfg_cache, _cfg_sig, _cfg_path = copy.deepcopy(data), sig, p
         return data
     return {}
 
@@ -1254,7 +1254,7 @@ def _load_cfg() -> dict:
 
 
 def _save_cfg(cfg: dict):
-    global _cfg_cache, _cfg_mtime, _cfg_path
+    global _cfg_cache, _cfg_sig, _cfg_path
     from utils import atomic_roundtrip_yaml_save
     path = _active_config_path()
     # Comment-, ordering- and Unicode-preserving write (a plain safe_dump clobbered hand-written configs);
@@ -1263,9 +1263,9 @@ def _save_cfg(cfg: dict):
     with _cfg_lock:
         _cfg_cache, _cfg_path = copy.deepcopy(cfg), path
         try:
-            _cfg_mtime = path.stat().st_mtime
+            _cfg_sig = file_signature(path.stat())
         except Exception:
-            _cfg_mtime = None
+            _cfg_sig = None
 
 
 def _session_for_key(session_key: str) -> dict | None: