Holy macaroni!!!
If you play the browser version, itch.io should be saving all your data, which is carried on after the game updates. But for some reason there was another person whose save files disappeared too for some reason. Unfortunaly, there's nothing I can do about that ;-; (believe me, I searched A LOT). But it seems it's just the site being weird.
If you play the windows (downloadable) version though, just copy your "save" folder from the old version into the new one.