Lifetime subber here, I was just peeking in to see what's been going on with the game and I noticed this thread. I'd almost forgotten about this game, but the funny thing is that I very regularly check in with STO, because there's an almost constant stream of Dev update blogs, and along the way I just stopped checking in…
The very same happend to me today, three times in a row. Nemisis gets to 1/2 health then either falls through the geomitry or just despawns, freezing the quest where it stands after Cyberlord goes down.