So I made a mistake and started a new game with both Animated Morrowind Expanded, and abot's MCA version of Animated Morrowind expanded, thinking the latter was a patch for the former and that they needed to be run together.

After abot told me that this is not the case, and that I'm supposed to be running the MCA version only, I used Wrye Mash to remove Animated Morrowind Expanded from my game. I reloaded the masters and hit repair all, but instead of turning purple, my save game stays green. Does this mean the duplicate references have not been removed? Is there something else I need to do to make sure they go away and make my save game healthy again?

Any input would be appreciated, thanks!

Repair all does not fix duplicate issues if it is already duplicated. Here is what I did for missing objects and duplicated objects when I tried to edit my player home.

1). I took everything out from my storage in the mod's cells and moved to a dummy cell. Then I saved.

2). I went into Wrye Mash and removed the dependency of the mod (in the saves tab) which had the missing or duplicated objects. I pressed the Save button. Then I did Repair All. Once I loaded up the save with the mod loaded, I no longer had missing objects or duplicated references and everything was fine.

Best to save in a dummy cell (e.g. do coc "Mournhold" in the console) and do it that way. Otherwise, you have to select and disable all duplicated objects and that takes forever. In your case, it's best to remove the dependency on both mods and only load one mod or the other and not both.