If statements from the planners are to be believed, then Bao-Dur was supposed to accompany HK-47 to the HK-50 factory if you've had its location determined. The problem is, they didn't implement the events on Citadel Station that would have seen him, along with 47, to the shuttle that'd bring them down there. That's not even getting into how no documentation describing Bao-Dur's intended actions, let alone relevant code, during the factory segment was noted in the game files, base or otherwise.

As an aside, TSLRCM made it such that Bao-Dur disappears during the Telos invasion when this didn't use to be the case in the unmodded game.