@sleve_mcdichael now when I try and connect to my Pi from my PC using ssh pi@retropie.local (which you helpfully advised in another post) it just opens a black box for 3 seconds which then disappears before I can do anything. My PC and Pi are on the same network.

That seems a bit over-complicated. I'd maintain 2 sets of auto-configurations for the gamepads - one having a hotkey and the others without it - and switch between them by modifying the auto-config folder where RetroArch looks for the gamepad .cfg files, that folder is set in the main retroarch.cfg file.