Interesting, I did a little searching and found a blog post by Chris Avellone, the lead designer of KotOR 2, who outlined Bao-Dur's fate in more detail (look under Game Questions #2):
"Bao-Dur - we didn't have time to finish his thread, but if I recall (it's been a while), he was supposed to die on the attack on Telos to help HK-47 get to the HK-50 factory and shut it down to save the planet."
I doubt this helps any, but there you go.
Interestingly, that would have to mean that Bao-Dur lives if you don't find the HK Factory, but Telos would die to the HK-50s, I... don't think there's anything in the game files to support an HK-50 apocalypse for Telos, though.
Maybe in some future version you'll be able to resolve Bao-Dur's fate, even if it's just in a quick and dirty way. It's just odd that a main character flat-out vanishes during the finale, but I realize that's not your guys' fault. Oh well.