Save progress is saved under your user app data folder, not where the game is downloaded. You should be able to update without any changes to your save data.
nice! so that means I just need to download the newer versions as they appear right along with possibly deleting the older version, and this wont cause everything to be wiped? edit: or does the game auto update?
The game has a built-in update notification, but relies on you to download the new version yourself. If you like to download games through itch then they also have a program you can download that can manage most of this for you.
