Now keep in mind, there are a LOT of different ways to do things in the editor. This isn't the only way to do it, but this is probably how I would.
Create two levels, one for intact, one for messed up.
Go into the map you already have ready, and select everything. Hold shift, and pull the whole map upwards--waaaay upwards--until you've got two copies, one on top of the other, but far enough up that you wouldn't know it's floating up there.
Then just fix up the copy to look how you want, and presto. When you need people to move between it, have a door or something lead to the new version of the town, and have all of your actors set to teleport to a new, corresponding place.
That way, you have everything all on one level, and it's easy enough to switch back and forth without opening a separate level.
