So if I go in not wearing my power armor, everything is just fine. I ended up reloading a save game so I could complete the quest. I went in to "search for clues" after checking the caravan and the entire town attacked me, cept dan. My companion even attacked me, I wiped the town out and thought since I could use the workshop I would rebuild it as my own including a beacon. I go off and do some other things, I think abarnathy was being raided, cant remember. I saw on the minimap I already got a new settler. So i go back and he attacks me automatically. So I decide to complete the quest to see if that changed the ownership. I enter the tunnel to the compound and dan instantly attacks me. I search google and see its something about wearing power armor. So reload the save game prior to searching for clues, exit power armor, and everything went fine. And now, if I enter covenant wearing power armor all the NPCs attack me instantly as soon as I walk up to one. So now I have to keep in mine to exit my armor at the gate every time.