diff --git a/gns3server/config.py b/gns3server/config.py
index a0c2d8d5..2ada115f 100644
--- a/gns3server/config.py
+++ b/gns3server/config.py
@@ -131,14 +131,15 @@ class Config:
             try:
                 # migrate the server config file
                 old_server_config = os.path.join(legacy_user_dir, server_filename)
-                if os.path.exists(old_server_config):
-                    new_server_config = os.path.join(versioned_user_dir, server_filename)
+                new_server_config = os.path.join(versioned_user_dir, server_filename)
+                if not os.path.exists(new_server_config) and os.path.exists(old_server_config):
                     shutil.copyfile(old_server_config, new_server_config)
 
                 # migrate the controller config file
                 old_controller_config = os.path.join(legacy_user_dir, controller_filename)
-                if os.path.exists(old_controller_config):
-                    shutil.copyfile(old_controller_config, os.path.join(versioned_user_dir, controller_filename))
+                new_controller_config = os.path.join(versioned_user_dir, controller_filename)
+                if not os.path.exists(new_controller_config) and os.path.exists(old_controller_config):
+                    shutil.copyfile(old_controller_config, os.path.join(versioned_user_dir, new_controller_config))
             except OSError as e:
                 log.error("Cannot migrate old config files: {}".format(e))
 
diff --git a/gns3server/controller/__init__.py b/gns3server/controller/__init__.py
index 445fdaad..d546f9b3 100644
--- a/gns3server/controller/__init__.py
+++ b/gns3server/controller/__init__.py
@@ -128,6 +128,7 @@ class Controller:
             except (ComputeError, aiohttp.web.HTTPError, OSError):
                 pass
         await self.gns3vm.exit_vm()
+        self.save()
         self._computes = {}
         self._projects = {}