If the Zirax commander in the story section 'Pirates YARR' is not looted this appears to leave one without the recipe when the corpse is cleared. Also I was irritated to have my starter SV shredded while I was deep in the pirate base. Logically the Zirax could and should reduce your base to a smoking heap while you are looting some POI, but that isn't much fun, neither is being stranded in space. My response to finding the core so early was to make a game backup, so I ran the base a few times. Keep up the good work.
Thx for the heads up. Will need to find some fallback solution for this. For your SV: You might have gotten attacked by drones patrolling the area? Or by CV combat ships?
My SV was taken out by a pair of minigun drones. In my defence it is early in the game and I had only built my tiny scouting SV. No sign of any drones at all in 12.5.