After running the function, you can try switching the game to windowed mode (Alt+Enter) and back to full screen (Alt+Enter again), or Alt+Tab twice to back out and return to the game window.

You can also try running it via a Trigger rule instead of with the hotkey.

If those two things don't help, there's likly not much you can do. Some games just don't allow us to prevent it from receiving the "lost focus" messages.