diff --git a/backend/api_server.py b/backend/api_server.py
index fa5c583..2107bdd 100644
--- a/backend/api_server.py
+++ b/backend/api_server.py
@@ -212,7 +212,11 @@ class APIServer:
 
         @app.put("/api/config")
         async def update_config(update: ConfigUpdate):
-            engine_reloaded, message = ctrl.apply_settings(update.settings)
+            import asyncio
+            loop = asyncio.get_event_loop()
+            engine_reloaded, message = await loop.run_in_executor(
+                None, ctrl.apply_settings, update.settings
+            )
             return {
                 "status": "ok",
                 "message": message,
diff --git a/backend/app_controller.py b/backend/app_controller.py
index 77b637d..d11670f 100644
--- a/backend/app_controller.py
+++ b/backend/app_controller.py
@@ -608,8 +608,17 @@ class AppController:
         Returns (engine_reload_needed, message).
         """
         if new_config:
-            for key, value in new_config.items():
-                self.config.set(key, value)
+            # Flatten nested dicts into dot-notation keys so we merge
+            # individual values instead of replacing entire sections
+            # (e.g. remote.mode instead of overwriting all of remote)
+            def _flatten(d, prefix=""):
+                for k, v in d.items():
+                    full_key = f"{prefix}{k}" if not prefix else f"{prefix}.{k}"
+                    if isinstance(v, dict):
+                        _flatten(v, full_key)
+                    else:
+                        self.config.set(full_key, v)
+            _flatten(new_config)
 
         # Update web server display settings
         if self.web_server: