If you just kill a random scribe they’ll be non-hostile after 3 days, so you need to make sure the person you kill is irreplaceable. You need to make yourself permanently an enemy of the Brotherhood of Steel in your own right. These essentials will NOT respawn ever again. They will respawn for later but I think the priority is to kill HIGH RANKING ESSENTIAL MEMBERS like Elder Maxson, Ingram, Kells etc. I cleared out the entire Prydwen from the inside out, including the Airport. Dismiss Danse and go to Boston Airport so people aren’t hostile.