Having spent a few hours yesterday trying to get to the bottom of this, I'm hoping posting here will help me understand my situation better. I've recently returned from a long hiatus from the game. I left soon after RotHC was released, if I recall correctly, and just before strongholds were released. So many things have changed in that time, but my issue is arising with companions. I understand that influence has replaced affection. However, the companion missions that used to be gated by affection don't seem to be similarly gated by influence. Also, I've completed every planet's story arc and my main jedi consular storyline all the way until I'm meant to begin KotFE.
Upon clicking the KotFE starter quest thingy on my ship, it warned me I might not be able to finish my companion stories after that point, I would get different companions, etc. So I stopped without proceeding, wanting to finish my companion stories. My jedi consular legacy shows only one of those five companions being unlocked, and indeed, it seemed like Tharan's storyline was the only one that completed.
So my issue is: what am I missing here? How do I get these other companions to begin talking to me again? Any help would be greatly appreciated.
P.S. Also, possibly of note: Sometimes my companion will have the ship symbol on their picture during solo flashpoints, telling me they'd like to talk back on the ship, but as soon as I'm out of the flashpoint, it disappears and there's no conversation to be had on the ship.