Did something similar but it was me removing the .zip file containing the game after submissions closed. Can't undo it either lol. I think we're out of luck given it'd be impossible to tell if after-deadline changes were made to the files you upload aside from fixing the load problems, and it'd be unfair for those who got it working and uploaded beforehand.
I say go ahead and fix the loading problems and when the jam votes are over you can upload the corrected version. Not sure what tag the jam is meant to have but if there's a tag everyone's using for their entries you should add it to your project's page under "Tag" so it helps associate the game being a part of this event.