Seconded - This just happened to me when I tried to make 2nd project from scratch with new names, new tiles - ect. My assets, sprites and more from the first game seem to be there but my map was wiped. I had been working on it for 100+ hours.
I found the "map.eem.backup" file. Problem is I wasn't able to do anything with it, I renamed the extension but couldn't get it to load in the editor. Please let me know if I'm going about recovering this the wrong way.
What a shame! I want to add that his certainly seems to be linked to creating a new game project. I'm afraid to work on two simultaneously now.