You can try using the Itch App which will update the game for you after you install it again using the app.
Otherwise just download the new version, install it, open it, and your saved games are all still right there. Saves are stored in a different folder on the computer, so even if you delete the folder with the old version of the game, your saves are still available for the new version to use.
In either case you'll still have to download the game again at least one more time, but your old saves are preserved without you having to do anything extra.