ROMs folder has disappeared from my PCs view but RetroPie still works.

[sharp3d]

I am a complete novice Raspberry Pi user so please explain it like I'm 5. It wont hurt my feelings. :)

Thanks in advance for responding.

I have a Pi 3 Model B running RetroPie. I built it about 6 months ago and run it using two 32GB micro SD cards. One is used for the OS and the other I load all the ROMs on to and connect it to my Pi and PC to transfer ROMs using one of these USB microSD adapters http://a.co/0HVigPi

I must have transferred ROMs to my PC dozens of times by removing this USB adapter back and forth without issue. A couple days ago I decide to update RetroPie to the latest version and accomplish this without much issue. I also run the scraper for the first time to get all the meta data for my ROMs(about 7,000 games worth). Up until this point I only had cartridge based console ROMs running on my setup. I decide to try and get Sega CD to run because it's one of my favorites. I was a little disappointing that there was more to the setup than just dropping Sega CD bin/cue files into the Sega CD ROMs folder and having it work like the other consoles do. However, I finally figure it out and get the Sega CD running. I only had 5-6 Sega CD ROMs on the SD card at this point, 4 out of the 6 worked, got just black screen on 2 of them. Not a biggy though, I figure I'll just grab those ROMs that didn't work from another source and transfer a bunch more since I sort of got it working. Well the next time I plugged this Micro SD Card into my PC using the adapter I linked above, my ROMs folder had totally disappeared. In the retropie folder I see BIOS and configs folders and in configs there is from_retropie and to_retropie folders. I checked to see if the ROMs folder had been hidden somehow, but it just isn't there, however when I put the card back into the Pi it functions normally and games will play.

I tried googling to see if it was an easy fix before bothering the community, but all I could really find were things about drive formatting fat32/ NTFS and people complaining that USB sticks(which I'm not technically using) are buggy etc... The card in question is currently formatted FAT32. I didn't do anything to reformat this card and I can't imagine the card reformatted itself to a format my PC can't read. Plus if it did, why am I still able to see some folders on this card. I'm really hoping the answer isn't formatting and reinstalling everything, but before I do that I wanted to see what you all thought?

Thanks!