well, try downloading the game on your desktop and see if it automatically finds and shows your saves when you try to load (so no itch launcher), if it does, your saves should be safe... and you can probably just play like that, versions don't have to be kept for saves to transfer over, so it's not like you'll have dozens of gigabytes eaten by ToS.
after that, if you reaaally want to use the itch launcher, you can overwrite your saves and delete the build over there to see if a reinstall fixes it, but that's for later, try what i said above.