If nothing went wrong you should be able to keep your saves.
On Android it will only delete your saves if you uninstall the apk instead of updating it.
And on computers the engine makes a copy of your saves somewhere else, so you can delete the old version and download a new one.
Also, if you're on computer I highly recommend using the itch.io launcher to manage the game, also makes it easier to update since you only download the differences and not the entire game.