diff --git a/tools/mcp_tool_registration.py b/tools/mcp_tool_registration.py
index 2170d8120a..5a16e82201 100644
--- a/tools/mcp_tool_registration.py
+++ b/tools/mcp_tool_registration.py
@@ -10,6 +10,7 @@ from dataclasses import dataclass
 from types import SimpleNamespace
 from typing import TYPE_CHECKING, Any, Callable, Dict, Iterable, List, Optional
 from tools.mcp_tool_common import _parse_boolish, _core, _resolve_tool_timeout, mcp_field, mcp_server_enabled
+from tools import mcp_tool_config as _config
 from tools import mcp_tool_handlers as _handlers
 from tools import mcp_tool_schema as _schema
 from tools.mcp_tool_handlers import (
@@ -461,13 +462,24 @@ def _register_connected_into_current_scope(servers: dict) -> int:
     if scope is None:
         return 0
 
+    # Callers that connect a subset (plugin go-live, a connector, orphan re-registration) pass only
+    # those names. A name they omit is judged against this profile's own config, or connecting one
+    # server would strip every other server's tools from the profile while their connections live on.
+    with _core._lock:
+        omitted = {_key_name(key) for key, scopes in _core._server_tool_scopes.items()
+                   if scope in scopes and _key_name(key) not in servers}
+    profile_servers = _config._load_mcp_config() if omitted else {}
+
     with _core._lock:
         stale = []
         for key, scopes in _core._server_tool_scopes.items():
             if scope not in scopes:
                 continue
+            name = _key_name(key)
+            if name not in servers and name not in omitted:
+                continue  # attached after the config read; the next pass judges it
             server = _core._servers.get(key)
-            config = servers.get(_key_name(key))
+            config = servers[name] if name in servers else profile_servers.get(name)
             cross_profile = _key_scope(key) != scope
             if (config is None or not mcp_server_enabled(config) or server is None
                     or getattr(server, "session", None) is None