The thing is that your game won't generate a new one if you start with the trivial script, the old one will just be replaced and the game won't think to make a new one.

If you make changes to the map files and wish to make a new map.rwm, you'll have to delete your old one, start the game without the trivial script (ie make a old-fashioned shortcut that goes directly to EB), then copy the new map.rwm that is generated to the backup folder. With the new map.rwm in both locations, you can then start using the trivial script again.