The bug can be reproduced if you keep on making changes to the 3dn file i beleive. It was working fine when i was working on it yesterday, but now whenever i try to add any more changes it seems to just erase my progress. More specifically i was working enemies in later areas.
I had been going back through my backups and they seem to work up until backup 6, 7, 8.. ect, wich had more changes done to the file.