Same problem but with all pirates, only hbosses are unaffected.

It seems random too, some of them despawn and others do not, but the majority come out, go GUAGRH then dissapear with their loot dropped on the floor. so somethings is killing them.

i've ran unto that while doing the ruin hatchery, and i am inclined to believe the cause for that is due to the amount of repeats one must be doing to a specific level or Epsode.
I have witnessed starbound breaking itself while i play for more than 4 hours a day, wich result in some funny or anying situations, depends of what your're doing currently.

Do you have Supper's Combat Overhaul? I was doing some testings to see which item of my modpack was causing this issue, and found out upon installing SCO all the mobs on FFS missions die as soon as they spawn.

@-book horse-
I do have it installed, thanks for the help