I assume this was a bug, as there wasn't even an announcement telling me of it.
On a precursor system, after I seemly cleared it, I made the excavation post and got my warships back to Terra. But so it seems that there were more precursor ships, and they landed a few troops, who destroyed my anti-robot force there (only a mixed brigade, plus one engineer battalion). So I sent back my warships, and diverged a troop transport to take a full brigade of heavy assault battalions there. The warships arrived much faster, so after destroying the precursor ships, I parked the ships on orbit and shot a couple missiles at the precursor ground troops to properly weaken then. So far so good. Advance a couple months in game and a few days out (playing other stuff) I go check my battle group to shoot a couple more missiles at them while I wait for the troop transport to arrive (it's pretty slow, plus it was picking up the garrison in a far away asteroid that used to have a civilian mining station). When I open the TG window all my ships had vanished. After wondering about it for a while, I spawn back my warships using the SpaceMaster, since my last DB backup were a couple in game months old, with quite a lot of NPR combat in between there and my current date, and when I turn on the sensors, it shows 8 ships with the exact characteristic of mine (which are pretty rare, ridiculously high armor, low thermal emissions, exact same sensor range, etc. ).
Right now I'm in the process of cleaning them up with my newly spawned ships, and they don't seem to be doing anything (except fire the anti-missile missiles, but I had launchers set to PD mode). It's also quite annoying to destroy, as I don't have any meson weaponry, and each of my ships take around 50-60 missiles (WH 16 each. Yeah, I seriously exaggerate on the armor department. It is 12k tons, with 20 thick armor).
So any idea of why my ships suddenly and stealthy became became precursor owned ships?