For the duration of the jam's voting period you should keep the original jam-version of the game available for download on your itch page. If you want to upload an updated version you should make it clear which is which -- for example, name the new version "postjam version" and the old "jam version". If I remember correctly: uploading a file with an identical name to the old one will replace it, so be sure to name the file you upload something different.