So during the update tests, I copied my old retrofe folder to my desktop as a backup. I was testing some things out with the 9.0 update using the backup. When I decided I wasn't going to update, I deleted the backup folder.
I resumed my work on setting up a ps2 emulator in the main folder and when I went to test it out, I discovered that only my NES was displaying games. I checked the snes settings and found that I had forgotten to change the copy of the gba settings to coincide with the snes instead. After fixing that, the snes displayed properly, but now my N64, sega genesis and master system, ps1, and gba are all no longer showing any data or games. I checked all of their settings and found nothing wrong that I know of. They are all set to the proper consoles and emulators. In fact, most of the time the background is blank, save for the layout image background, but when it's not, it seems to display the games from the last selected emulator on the wrong menus.
The one in the photo on the bottom left that's blank is the N64. I checked the N64 collection settings and everything appears to be in order.
I was thinking it might be the modifications I made to the layout, but that was weeks ago and this only started since I was testing the new update on the backup.