That´s right.
Ever since I got the itch client, I download all itch games through that, instead of a browser. I thought that method would be the least troublesome one, but I might be wrong about that. "In that case maybe it’s deleting the save folder after each update?" I think you are right, since that seems to be what have happened. That have just not happened with other Itch games.
Sorry if I am being difficult. I actually have a lot of positive things to say about the game, I just wanted to report a (potential) bug first.