src/Ryujinx/AppHost.cs

@@ -586,6 +586,9 @@ namespace Ryujinx.Ava
             // (resets custom settings if there were any)
             Program.ReloadConfig();
 
+            //Updates the gameList (changes the status of the user setting if it was added or removed during the game)
+            RyujinxApp.MainWindow.GameListUpdate();
+
             _isStopped = true;
             Stop();
         }

src/Ryujinx/UI/Windows/MainWindow.axaml.cs

@@ -645,6 +645,11 @@ namespace Ryujinx.Ava.UI.Windows
             ReloadGameList();
         }
 
+        public void GameListUpdate()
+        {
+            ReloadGameList();
+        }
+
         public void ToggleFileType(string fileType)
         {
             switch (fileType)

src/Ryujinx/UI/Windows/UserConfigWindows.axaml.cs

@@ -108,7 +108,8 @@ namespace Ryujinx.Ava.UI.Windows
         }
 
         protected override void OnClosing(WindowClosingEventArgs e)
-        {   
+        {
+            InputPage.Dispose(); // You need to unload the gamepad settings, otherwise the controls will be blocked
             base.OnClosing(e);
         }
     }