@stevepax Hello and belated welcome to this forum. I'm close to finishing my own arcade cabinet myself and I plan to do something similar to you but with two bluetooth controllers for players 3 + 4. I didn't dive into the matter deeply yet, however, but I'll try to answer your questions to the best of my current knowledge.
If the emulator and the game rom support four players, you should be able to configure the controls for players 3+4 just like those for players 1+2. Mind that some games come in different versions (roms). TMNT has 2 and 4 players versions, for example. Its 2 players versions have "2p" in their rom names.
At least Retroarch should recognize your controllers upon reconnection. A common advice is to connect them every time to the same usb ports in the same order. There's also a script by
@meleu called
joystick-selection that simplifies the mapping of controllers to players, and if the controllers should be recognized by their names or by the ports they're plugged into.
Alas, I don't know.
You're rightly terrified to lose your configuration if you didn't backup it recently. Do so now, because bad things happen all the time to "valuable" data, e.g. storage failure. (I put "valuable" in quotes because there is a saying that data with no backups isn't important by definition; if it were, it would have backups.)