I think there's a way to get around that. The game references every region by a number. I used those numbers to construct our MM8 site, so if you look at the link to (for example) the reference section on Regna you'll see that it points to 'rr13s.html'. Regnas's number is 13. Changes that you make to a region are saved in a file somewhere in the MM8 directory structure. Regna's file would start with 'r13', iirc. Deleting the file with the changes would force the game to create a new file for the region the next time you entered it.

NB: Make sure that your party is NOT in that region when you delete the file. If it is then the game will just save your changes to that region based on your savegame file. (In fact, a savegame file is just a file of the region or dungeon that your party is currently in.)