After I did a rollback on my computer, all the map files, monster files - basically every blue image file that was stock disappeared! They still exist in the other games I've created but in the most recent project everything is poofed. The map sizes and the custom images are all still there too.
Edit: all default sound files are also gone.
Update: I was able to copy paste the "blank" maps into a new file, and all the maps complete with events showed up. I was also able to copy paste all my edited script, although I had to manually transport all the new created files and haven't yet fully changed all the basic system edits.