Well let's see in k1, Bastila's options are 1) Death doesnt matter where 2a) Alive redeemed no romance 2b)with romance 3a) DS as Revan's apprentice, lets face it Malak was weak and no one seemed better to be your apprentice.
So, 3 out of 4 she's alive and with Revan, unless Revan kills her. I think she shouldn't make an apperence or mentioned without Revan if she is alive. The problem is to deal with all possible outcomes that could be alot of dialogue. I don't think they'll kill her off in that lame no real point kind of way if he survived k1. If she does show up in k2 it's probably is Revan related.
Speaking of npc's I don't see HK-47 leaving Revan's side unless order to do a mission. If Revan ended LS can't be an assassination mission but DS it could be.