Follow this up with a 'Repair All' to remove any debris records (globals, npcs, etc.) associated with the removed mod.

Note that if you use Mash to remove a mod from a savegame's master list, you automatically remove all of the references placed by that mod.However, note that ref removers will also reset/remove any legitimate copies of those items, so be careful! If there are other objects which are repeatedly doubled in your files, then you may be able to create additional ref removers for them.I.e., if you lock-picked the door, you'll now find it locked again. However, it will also reset any other doors. Since doors are particularly prone to doubling, removing door references will have the effect of removing all door doubles. Wrye Mash does have the ability to remove a specified set of references from the game.However, it will not fix doubling that has already occurred and it will not fix doubling that is already locked into the savegame.Doing this will fix bad references, orphan contents and debris records.Simply go to the saves tab, right click on the problem save file and select Repair All. Fortunately, many (but definitely not all) of these problems can be fixed with a single menu command on Wrye Mash.

Morrowind save files can become corrupted in a number of ways:

Skyrim save game cleaner mod