Two places to look that could get you working:
Get rid of SNES here:
/opt/retropie/configs/all/retroarch-joypads/
Look here: I think I’ve seen people recommend removing this file and letting emulationstation rebuild (but look inside first)
~/.emulationstation/es_input.cfg
Caution: but maybe something here.
/opt/retropie/configs/all/retroarch.cfg
