I don't think there's any way to submit after the deadline. It's handled by itch.io so even the host can't help, afaik.

But on the note of your issue, for future reference; it's usually just the project.gmx file (not the gmx directory the files are in) that gets messed up. It can get messed up because just 1 file failed (image, script, path, etc), even silently, in some way. After such an issue it ignores the other files and saves it anyway. The project.gmx file is just a list of all the other files in the project. Instead of putting all the files back manually in the IDE, you can add the file paths to that one file and it should then load them normally again.

Also, upload your game anyway. There's no prizes for the jam, so you've still got the best out of it, which is learning and experience. :)

Thanks Jack, but I thought I couldn't upload it after the deadline had passed.  It said "submissions are closed, judging is happening".  A lot of things are bØrked after this problem and it will take a day or so to patch it up.  

I was also thinking of re-constructing it in a clean file and then streaming it on twitch.  I need to learn how to use twitch anyway.