I went back to an earlier save, and as near as I can figure it, what happened was that I got into a too-heated battle and my other companions decided to take off. I gather this because in another battle I lost all but one companion, but I could still see the rest of them in the vicinity (they hadn’t been destroyed), and yet I couldn’t order them to follow me any more–the game said they weren’t part of the player fleet. So maybe there’s a morale mechanic?