Theres the autoconfig file in
opt/retropie/emulators/retroarch/configs/yourgamepad.cfg that is created when you do the retroarch joyconfig. Then there is the retroarch.cfg in
opt/retropie/configs/all that is set up for all retroarch emulators and then there is also a retroarch.cfg file for each individual retroarch based emulator in each respective folder in
See this wiki page on controller configurations
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