I have found that after getting a ſatellite from beating a boſs (like the Henterpriſe) if I log out during the warp phaſe (warping to the next ſtage), when I log back in the newly gained ſatellite is gone, like it’s not ſaved upon logout.
When you log back in, you resume your mission at the wave AFTER the boss, right? Or are you brought back to the boss again?
Idk about him,but I do resume the mission after the boss,yes. However,since technically,you collect the satellite after the boss fight,the game doesn’t save it until you finish the next wave.
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Ah, yes. Correct 
. Progress is saved first, then you collect the satellite. So satellite will be saved at the end of the NEXT wave, and if you quit before then you will lose it.
Yep. Can be annoying,but it prevents farming satellites in a single wave.
Yeah, it reſumes at the next wave. I think it would be nice (if poſſible) if there were an “intermediäte” periöd between two ſtages including the warp, ſaving any changes during this periöd, or maybe juſt ſaving things on logout.