I do not know if it was the padawan healing him, or himself, but I only managed to kill the jedi once I started kiting him around the room, he stopped regaining health then. Other than that I had some non-los foes, but Mako took those. I never go back to the med center in such instances anyway, I always probe, so I did not encounter that bug.
I built the jetpack, then simply moved towards the engineer, rightclicking it in my mission inventory until it lit up.