Hey, sorry it took a little longer than I'd like it to.
The root cause of the issue was bad interaction between the forced cinematic and the messagebox that usually controls if you change motherships or not, its a pretty known problem that may even still be alive and kicking for other story routes FYI.
But it seems to be working now, heres the fixed storyline file:
[Replace at Star Wolves 3 Civil War\Data\Scripts\Quests\mission_19a]
https://pixeldrain.com/u/aaUR7cc6
Happy piloting
