That happened to me once and I was the only one left of my crew when it did. I tried bouncing from ship to ship to see if I could aim at him.
I finally did end up killing him off though. If you go to the very back of the boat on the Col by the helm w/your staff or dagger, you can aim down and look for the red target. Once you lock on him, fire away. My staff was only lvl 3 I think when I this happened to me so it took a while for me to kill him off since he was a lvl 35. And anytime I went to "vent" about it in chat, his health seemed to regenerate.
So, just wanted to let you know that when they do glitch off ship, your efforts do not have to be wasted by logging.
