Ok, so went to start minecraft today  been a while since I last played but never had the issue in the past. My second display went out when the game went to game mode. So I closed the game and it didn't come back up. Checked the display settings. The system no longer seen the second display at all. In fact it didn't come up with a reboot. So powered back down. Checked the bios settings and then removed power from the display. This time on rebooting it came back up.

I develop software using Opengl, DirectX and vulkan. And I've never EVER created such problem. I don't even want to guess what you did but whatever the hell it was its wrong.
Full screen game mode doesn't require the second display being shut down. In testing it only makes about a 3fps drop leaving it open across games. If you are worrying about a 3fps issue you are focused on the wrong issue in  your game engine. Suggest you learn to properly profile your game engine even if it is threaded it can still be done. Hell I can profile the game engine i have which uses a task manger to grand central dispatch. With all your expertise there you sure as heck should be doing better than this.
You might want to put the option back in to run in borderless window mode. I'm pretty sure most of your players/ customers would prefer having that option over this type of garbage.