this is a rather simple procedure, but I will explain in the best detail I can to make sure you don't miss a heart beat.
First, let me make you feel embarrassed by pointing out your mistakes. First of all, moving the interior does nothing to effect the exterior. Duplicating the interior again solves nothing, just makes things a little messy. So, if the interior of the house you want to move is finished to your liking, leave it alone. Don't touch it.
Now, to fix this problem is easy. If you have saved since the conflict began, then all you need to do, is launch the game with the mod you are editing deactivated. When you load the game profile, save, and quit out, and re open the construction set. This process is called clean saving and is required by many mods that are being updated from old version and it is highly recommeneded you do this anyways if you are updating from an old version.
Now in the CS, make your edits again by moving the house to the new location, save the .esp and exit out of the CS. Open the Oblivion launcher and activate the mod now, run Oblivion via OBSE (unless you do not have OBSE installed) and then load your game! Tuh-duh, things should be how you want them now.
On the other hand (as you already mentioned) if you have already made the changes, all you have to do is make a new save or overwrite your existing save file with the mod deactivated. After savign open the launcher and activate the mod again, and things should have the same result.
The constuction set is filled with bugs left and right, so the clean save is to eliminate a small glitch (bug) that is caused by the CS.
EDIT:
oh, and be sure not to save your profile where you place the house. When you activate the mod and load, you will be stuck inside the mesh of the house. The same applies if you move and interior of a house, be sure not to save while in the interior as you will get stuck falling in an endless abyss.
Should this happen and for whatever reason you cannot fast travel, just open the console and type in
coc testinghall;note it's spelling: COC(space)TESTINGHALL
you can use coc with any place but they all have specific ID names that you have to use for the game to recognize. Example, is Vilverin's ID is vilverin (simple huh?) so you would type: coc vilverin
if you coc to the testing hall, be sure to exit it via Hawk Haven door (should have a green light on it) and from that point, you can fast travel anywhere.