"For web sideloading: simply upload the new zip file and your Playdate will automatically patch the game." I can tell you that it does not work in this way if you downloaded the game originally before February of 2023.
There's a giant big blurb on the sideload page with instructions for how to copy your save file over to the new format if you played before Feb 2023. https://help.play.date/games/sideloading/#duplicate-games