sigh ok i have run into this also, and it can affect vanilla npcs as well. the only "fix" (it's actually a workaround) i found is time consuming and requires the use of the console (and something to keep notes on), and it is  time consuming     while not the most elegant solution it does work (for me at least) and prevents the NPCs are now "arch-enemy" when they should not be and it prevents that from messing up custom followers (those with their own follower
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