Same thing here. This is basically a game breaking bug. After replaying chapters lost indefinitely: Jaesa and Pierce. Also several other companions are listed twice! Under "Unavailable Companions" and "Other Followers/Main Characters" - 2V-R8, Broonmark, HK-51, Vette. Also listed is Malavai Quinn - but this is normal since I did not bring him back from the Companions Terminal on Odessen. I'm afraid to replay any of the chapters - I don't want to lose more high level companions. Also, all are 25+, this is a big problem for crafting...