So i haven't played in a while, but i've kept the game updated using itchs desktop app does that break the game with Arcadean saying to not overwrite the game? is part of my game gonna be bugged?
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The Itch app automatically does some sort of wizardry that keeps the game safe. I'm not a programmer, I don't understand it, but it works fine. No worries.
(I will add, however, that because of some of the changes, some very old saves do not load properly and just throw up an error, even if you did follow Arc's suggestion of a fresh download. Use the "rollback" option until you find a save that recovers.)