Hm... when you import resources, do you directly put them into the folders, or do you use the importer? Because I've seen a problem on different forums that projects went corrupt because of this.
Or did you accidently paste another game's map tree into your game?
When I import resources, I make a new folder in the RM2003 Projects folder and paste data from the .lzh. As far as I know, I never pasted data into this project folder. I save frequently, and all of a sudden, my project rolls back. If it helps, I can tell you some of the things that got erased from my vision
-Monster data from a new area I was working on
-The names of some towns I created (for teleportation purposes) were renamed to their default state.
-A whole dungeon got deleted (although luckily, my spare project kept that.. but I have to re-assign the monsters)
This could actually be a good thing because my development gotten a little shakier from that timeframe of lost data, but still... that's freaky!
But let's suppose the map tree got corrupt and the maps are still there... would there be anyway to re-detect them?