I'd think you can do that but upload them as separate files, don't make the new one the webGL build that runs by default and mark the updated one clearly showing that it's not the one to be judged on. Just my 2 cents.
but this is not good I want to show in the web-game the updated game not the original
you can change it as much as you like once the rating period is over
XD I know That LOL
I know it may be frustrating to forget or not being able to add something to your game, but the point of the game jams is the time.