Simply put, the “Rebuild your base at flared location” command should be put as highest priority when giving it to an AI. It’s just so stupid when an allied AI is being overrun by enemies, and you tell it to rebuild it’s base somewhere else, but it keeps sending its villagers to die trying to rebuild buildings where the enemies currently are.
Giving this command should make the AI forget all other tasks for some of it’s villagers (Or all if there are few left) and then go and rebuild at the flared location without any hesitation.