Keep your "survivors" in a safe place to start with.
Go into RMXP and create a map for every one you have (if you've got a Map239.rxdata, then you'll have to create 239 maps - I haven't found a way to skip any). Just leave it as the default size and tileset - all you're doing is saying the game has that many maps.
Close down, copy your REAL maps and paste into the Data folder, replacing the existing "placeholder" maps you just created.
When you go back into the game, all your maps should be there, with the correct tilesets and all.
You may find if you've imported resources, changed tilesets (in appearance or in the database) that you might have to go back and do some of that stuff.
This method works for me when I just want to look at a map someone else has created, so hopefully it'll get you out of trouble