Star Trek CCG is still very much alive. The Continuing Committee (trekcc.org) still produces new virtual sets for both First Edition (1E) and Second Edition (2E). There are groups of players throughout the world who still compete in 1E and 2E tournaments. If you're still interested in the game, check them out!
It's happened to me several times now. What I've noticed: I can start the run with the skill bar correct. If I die, regardless of playing Borg or not, my kit abilities disappear from the skill tray. All the other spaces are fine (such as orbital chasing beam, revive ally, pets, etc), which leads me to think it's something…