If a base hasn’t had interaction from its builder in a certain amount of time send that player a warning that it’s about to be marked as fair game. A few days later, if no action has been taken, mark it as abandoned and free to loot. Possibly with quests to access this looting feature. A Scavengers’ Guild?

If you get a bug there are a lot of solutions on their Discord. The join link is on their main page: https://fallout4london.com/