I got to The Vault, called for the friendlies (F), killed everything, the friendlies are here, including the officer. There are no enemies around but the friendlies are hiding. I waited a long time, enemies arrived and I wiped them out.
And yet... it still says "Friendly takeover in progress" and the friendlies are still cowering.
I googled and it seems that this is an old issue that has not been fixed, so I have zero hope that the devs will fix this problem.
So... does anybody know of any tricks to trick the takeover to complete?
UPDATE: Answering myself... I went on a patrol rampage killing everything on a 1-block radius. When I got back I found the team defending, killed them and done.