right click on the icon and you should be able to see the source file which for DX11 is "aceshigh11.exe"
Check under the mapping to see if the right mouse is set as your mouse in the game. Its really odd that it would lose connection with the game like that. I think you can get there by using tab to move the active buttons.
You could also navigate to the "settings folder in the file manager, rename it to "settingsold" or something. Unplug your controllers and then start the game. It will rebuild the settings folder automatically. Then go into the game and see if you loose the mouse again. If you dont the controllers are messing with the setupor you have assigned an axis to both your controller AND mouse.
Plug in each controller you have one at a time to see if you lose it again.