I wish I had some better news for you, but that's an 8MB file I can't figure out. I ran this game both with your 3DN first and then once again with no 3DN file and both times it was exactly the same as if nothing had been saved to it.
Now that it's up, geod might have an idea about what's happening here. I've worked quite a bit on about 10 games so far and nothing like this has ever happened to me yet. I'd really love to know how this happened and work under a reasonable assumption that it won't happen again.