I have a related issue with the Switch Pro Controller and Bigbox. When I run any emulator the emulator hooks into the Switch controller, completely taking it over. I then have to use the keyboard and mouse to clean exit the emulator, but the emulator doesn't pass the controller back to Bigbox. I have to turn off the controller and turn it back on again while in Bigbox for it to rehook.
I would be happy to autohotkey this process but happier for it to be addressed in development since I don't know if I can get around the rehook process using AHK (turning off the controller and turning it back on again).