Yes, after the rating period has ended you can upload updated files to the project page. It's nice if you keep the original jam version there for posterity.
I'm gonna make a second itch page for updates until after the event and then update the original. I like it done this way a lot better than other jams because I think its common for the ratings of more recent versions to take over the ratings of the original version so its not really a 7 day event anymore.
