So i have tried creating a new profile like you suggested, and i thought it worked, but then i noticed the children at the scene when wendigo removes her collar and blows up, they all flag hostile, and were still hostile in the row boat, i have tried this with several races and characters. my roommate is trying as well and his go hostile at the fight with the voidwoken on the deck of the ship.
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and now after several hours of testing we have discovered 2 different mods;
Initiative fix, for our roommate who plays the mod class chronomancer
Massive skill re-balance
are the two mods causing the NPC's to tag as hostile.
one of us will be notifying the mod creators that there mods are incompatable with eachother so others dont have this problem