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.)