@baviaannl The keybindings are stored in different files depending on how you saved them: globally, per core, per game, hardcoded, or as a remapping. See the docs about controllers for details.

Since remapping shouldn't alter the retroarch menu keys, I think you've saved your keys hardcoded in one of the possible files called retroarch.cfg in the directories /opt/retropie/configs/all/ (global) or /opt/retropie/configs/neogeo/ (neogeo core). In these directories, there should also be files called retroarch.cfg.rp-dist with the default settings. To reset your settings, replace the file retroarch.cfg with the file retroarch.cfg.rp-dist in the same directory. This can be done from Retropie's command console that you land in if you quit Emulation Station without reboot or shutdown:

# make a backup copy of your global settings cp /opt/retropie/configs/all/retroarch.cfg /opt/retropie/configs/all/retroarch.cfg.backup # replace current global settings with the defaults cp /opt/retropie/configs/all/retroarch.cfg.rp-dist /opt/retropie/configs/all/retroarch.cfg

For your neogeo core settings, replace all with neogeo in both command lines. (Four times all, two on each line. The lines beginning with # are just comments.)

I'm a total newbie about to make a very simular setup, so I wonder if this is working out for you or there are any problems?

Having one insert coin button (and not two) , and 2) having it double as select. Having Hotkey and Exit Emulator set to the same button?