Well, like I've said elsewhere, this is one of those situations where balance and story for a computer game comes up hard against established canon in the main (tabletop) universe. I personally think that core Shadowrun is going to be painted into a corner by the video games because of these things; as far as I can tell, the designers and writers for the computer games aren't double-checking core canon, and are therefore making shit up as they feel like it.
But still, this could be an issue with 'gotta keep the bargains you made'. Or just a lie; I don't imagine the long-term effects of her supposed departure are covered within the SRHK gameplay, so you honestly couldn't say one way or the other if she actually left, or simply appeared to. *shrugs*