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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.