I've had the exact same thing happen, five damn times in a row. Level 65 Jedi Consular. Beat their trained monsters, have the Mandalorians reset. Whole battle resets. Fought the same two damn Mandalorians. Again, and again, and again, and again. Companion vanished once; GSI droid twice. After three tries, I try to quit, but the game won't let me either log out or quit the game - still in combat, it says. So I had to minimize the game, and shut it down from there. Then it happens again when I go back. Two more times.
This didn't happen during my first play-through - Bounty Hunter, level 65. That was at least a month ago; been maybe two patches since then.
I had very much looked forward to taking my Jedi though this expansion, on to Ziost, and then into Knights of a Fallen Empire. I can't say that now. Frankly, I am giving very serious thought to just skipping Shadow of Revan. Which means Ziost? Fallen Empire?
I am going to try, one more time. After that, I don't know. I could just start the Knights of a Fallen Empire expansion, but I wanted to finish Revan, dammit.
This is not fun; it is raw frustration.