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Similar issue, I finished uploading to itch before the deadline, but realized 23 seconds too late that you had to also go back to the jam page to finish the submission. Is there a way to still get the game submitted?

Yeah, same happened to me here. That submission flow is very odd. It seems like you should be able to link a project to a game jam, so that any uploads you have done or in progress at the time of the deadline get submitted to that jam.