I started having a similar problem.
Everything was working fine since I got the system built and initially loaded. Playing Atari 2600, 7800, Neo Geo, SNES, NES, Genesis, SMS, and PSX. Tonight, I loaded a single PSP rom and upon booting the handheld, it no longer can find any of the games. I don't think its related.
I put a new image on the card, then reloaded ROMS, Saves and BIOS files, but still nothing. Also grabbed another card and the same behavior keeps happening. Both cards are SanDisk 128GB XC.
In all cases never lost files off any cards unless using Etcher to reload the image.
Installation of ROM, saves and BIOS files are done through a Windows 10 computer using "Linux File Systems for Windows" by Paragon Software.
Thanks in advance!