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I'm pretty sure you can still change the settings and say that it's not a browser playable game. Don't delete/re-upload your game, just change the settings to let us download the exe

If that doesn't work, send a message to the moderators of the jam and ask about changing your submission

I ended up deleting the original, then zipping the entire "Build" folder and uploading it. 

It's still not visible. If you can't see it, then others can't either. I imagine it's because you deleted the files. You should get in contact with the moderators