It looks like I lose some abilities from my character from time to time--and I saw it happen as I crossed sectors. Temporal Negotiator, which I believe is connected to my character, not a specific ship, is always available on my JHAS and Arbiter, but almost never on my Nihydron Destroyer. It was available once on K-7, then disappeared when I left the sector, and isn't even available on the abilities list to be restored to the ship. It's not precisely a load-out issue, because during the load out problems, the abilities were still available to be restored. It doesn't seem to be an issue with T6 versus T5-U, because my JHAS is a T5-U.
There are probably other abilities fluctuating as well, but Temporal Negotiator is the one I noticed first. (Maybe it's just something I don't know about that ability, but after adding it and watching it disappear from the abilities list--that just seems wonky.)
So, known bug? Needs /bugging?