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In Into the Breach, from the shopping UI after defending an island, does permanently assigning a pilot to an island in exchange for reputation remove the pilot from your hangar?

I don't want to permanently lose any pilots from my hangar for future playthroughs, but it seems like good option to trade in extra pilots for rep because otherwise they are just diddling around doing nothing.

I didn't see an explanation on wiki or blogs about the 'permanently assign to island' mechanic for pilots, can somebody who has tried it explain that please?

I would try it myself but I don't feel like cheating and since it is a rogueish-like I am fearing permanent consequences. (but please correct me if that is not the case, thanks!)

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No.

It removes the pilot from your current game and prevents you keeping them at the end of the run, but the pilot will remain unlocked in your hangar (as their lvl 1 version) permanently.

Note that this only applies to the pilots with special abilities. The randomly generated pilots from the start of the run aren't kept on your hangar anyway, unless you specifically take one to the next run.

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    Note the lore explanation: ever time you fail a run, you jump back in time. That also unwinds the "pilot donation", since you go back to before you started your game. (The unlock mechanics for pilots and squads sort of contradicts the time travel, but that's a matter of good game design over pedantic realism).
    – Flater
    Jul 5, 2018 at 8:15

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