@daubsi You shouldn't delete /opt/retropie/configs/megadrive/retroarch.cfg without re-installing a megadrive emulator after. We include a default config which includes the global retroarch configuration (from /opt/retropie/configs/all/retroarch.cfg).
If you remove the megadrive retroarch configuration and then run a megadrive emulator RetroArch will create a new configuration with it's defaults and that will contain incorrect paths and other settings.
the default config for /opt/retropie/configs/megadrive/retroarch.cfg is# Settings made here will only override settings in the global retroarch.cfg if placed above the #include line input_remapping_directory = "/opt/retropie/configs/megadrive" #include "/opt/retropie/configs/all/retroarch.cfg"
(I assume you mean /opt/retropie not /opt/retroarch in your post - i copy and pasted some paths and then realised so have corrected my post)