There’s an option in the RetroPie setup to give ownership of all of the ROM folders back to the pi user. Perhaps the folders themselves don’t have the proper permissions / ownership? I’m only guessing since I honestly don’t know for sure.

Maybe run a file system check on the SD card if possible?

Barring that, it might just be easier to backup all of your save files, ROMs, etc. to a safe location and reinstall everything (I know this isn’t anyone’s favorite exercise, but SD cards are screwy sometimes and starting clean does have its advantages).

Good luck! Maybe someone more knowledgeable than I can chime in.