I started with another toon, LS Sith Warrior that aligned with the Republic on Iokath. Koth and Quinn are gone from my companions even though I didn't killed Koth and Quinn joined me at the end of Iokath. Also its says that both Malcom and Acina are dead. Will this affect my choices on Ossus, what will happen if it says that Malcom and Acina are dead?
EDIT: Pierce, Broonmark and 2V appear twice on my list
EDIT 2: While it says that both are dead, it definitely saves your choices. I get dialogue about killing Acina on Iokath. Seems that all the bugs are with the companion list, not the story.
EDIT 3: I got back LS Jaesa, but I'm getting the Alliance alert for DS Jaesa