So, I have a plugin that contains an edit to a vanilla NPC I didn't want to make (call her Agnis). I could revert the change back to the vanilla state, but that would leave me with a dirty edit.

So, I set the Ignore flag on the appropriate NPC record in the Details screen, and load the mod ... and then get presented with a dialogue box saying that the FormID for Agnis is not unique and has been renamed as AgnisDUPLICATEXXX. Sure enough, on loading there is a new NPC record of that name, with a new FormID (BUT! the new FormID is in the 00 Skyrim.esm numberspace). This is marked as modified, while the original Agnis record is no longer modified. Great, I should just delete the new duplicated NPC ...

... no, because it seems that the CK has "helpfully" gone and edited loads of things that referred to Agnis to now refer to AgnisDUPLICATEXXX, and while the duplicate can be deleted and the mod saved, the CK issues plenty of warnings on loading the mod again.

Now, I used the Details screen and Ignore feature to delete the wreckage I could see (mainly, stuff I was sure my mod had no business editing because I didn't put it there), and the warnings went away, but of course I have no idea about any wreckage that may be lurking in records I did originally intend to modify.

So ... how am I supposed to clean a mod of unintended NPC edits, using just the CK, as that is all we have?

Edit: all this pertains to CK 1.6.89.

File > Data > Details, find the override, Del, save/exit.

Erm, that is what I just said is precisely what is not working.

Can you link the plugin? It sounds like your plugin is injecting the duplicate into Skyrim.ESM.

It's on the Skyrim Nexus, search for Diverse Muscle Tones (can't link to it directly as some of the user-uploaded images are advlt).

Ok, there are no duplicates. Agnis "Agnis" [NPC_:00020044] is the only Agnis in there and her override's FormID lines up with the original.

Indeed. What happens if you then set that record to Ignore in the CK and proceed to let the CK load it?

EDITOR: Editor ID 'Agnis' for NPC_ (0001A696) is not unique, previous object (00020044) is type NPC_. Editor ID will be set to 'AgnisDUPLICATE001'.

...and the override is removed, however AelaTheHuntress "Aela" [NPC_:0001A696] somehow had their EDID changed to Agnis, prompting the end result AgnisDUPLICATE001.

Removing 0001A696 resulted in the same thing happening to WERoad02NobleF [NPC_:00102D63] and she was renamed AgnisDUPLICATE001. Odd indeed. I'd remove the NPC group and start that part of it from scratch. Never seen anything like this before...

Has Snip ever been used on this mod?

No

Right. Reassuring to find that I'm not doing something obviously wrong, at least Thanks for looking at this.

Alas, doing the NPC group was by far the most consuming portion of the mod, and if I cannot safely back out unwanted edits then redoing those is going to take a great deal of care ...