ROMs disappear on reboot

[creepco]

Hello, I have been using Retropie on a Raspberry PI 3 for several months now, with no problems. Just today, any new ROM I transfer onto the PI disappears on reboot. I am able to play the ROM after transferring to the PI (and restarting Emulation Station), but when I reboot the PI any new ROMs are gone. The same thing happens if I delete a ROM: it disappears from the file system, but after rebooting the system it is back. This is happening for any file I add to the PI. It's like the PI is stuck with the current files, and will not retain any changes. I have tried transferring files using Samba and SFTP, and this happens with either method. This is happening for all files: I've transferred ROMs to NES, SNES, and PSX, and they all play until reboot, when they disappear. When I look at the roms folder on the PI the files no longer exist. I have used Samba to transfer files for months now with no issue. I don't know of any settings that I've changed. Ideas?
Pi Model or other hardware: 3
Power Supply used: Standard 2.5A I purchased with PI package
RetroPie Version Used (eg 3.6, 3.8.1, 4.1 - do not write latest): 4.2
Built From: Pre made SD from Retropie
USB Devices connected: None
Controller used: 8BitDo NES 30 Pro
Error messages received: None

[simonster]

That's a bit of an odd one. Most likely culprit is the SD card, somehow not writing the file table correctly. Are you shutting down correctly when you have finished (i.e. from the emulationstation menu, and waiting for the green light to stop flashing and go off, not unplugging it whilst still running)? If you are, I would suggest the SD card maybe suspect.

[lostless]

@creepco make sure parse parse game lists only is turned off under the start/other settings menu.

[DarkWolf]

@creepco I would recommend testing this out (-> @simonster ), otherwise I would recommend to (helped me) save configs and roms and reinstall retropie... I had some of those odd cases too

@lostless I guess this wouldn't change anything at all. The files are disapearing... so yeah

[creepco]

Thanks for the help and suggestions. I figured there was a decent chance I'd need to reinstall... I shut Retropie down through the emulationstation menu, but I'll have to make sure I'm waiting long enough before unplugging. I have had to hard shut it off several times when games have hung, but that was rare.