Hi. I think most game jams let you modify your game with hotfixes where the issue is game breaking in nature - the game jam's page doesn't seem to forbid it either. From what I've seen, a common  thing to do is to also include a note saying what the nature of the hotfix is.

You should be able to upload a new file for your entry in the following steps:

1.  Click the dropdown menu in the top left corner, and select "View profile". You will now see a list of your uploaded games/projects. 
2. Click the project that you wish to modify. You should now be in the project page of your project.
3. Click "Edit game". You should now be in the project's properties page.
4. Scroll down to the "Uploads" section. Click UPLOAD FILES.
5. Select the file that you wish to upload. Once the file has been uploaded, scroll down to the bottom of the page and click SAVE.

You should also view the page and download the file yourself to check that the correct files have been uploaded and are visible.

I hope this helps.