My story is similar. Before KotFE uploaded, I had finished tracking the target down and captured him, but had not yet finished the mission. After KotFE, imagine my surprise to see I had to repeat the entire final stages of the mission again. So I went to all the places again, found the clues again, tracked him to his hideout again and captured him..again. Then I met up with the Mandos on the space station turned him over and formally took on Torian as a member of the crew. Then... no trace of him at all.
And yeah, I'm a female hunter with whom Mako is trying to start a romantic conversation option.
Can't wait till these bugs are ironed out. My BH is on hold for now. Quesh can wait.