Hey this happened to me too! I would have lost so much info if I don't get this back...
I discovered a part of why it happened and luckily I had a recovery. The quick start guide shows that you need to export the game as
a browser version first and then run that through the cook tool. I wasn't doing that before, which is why I think in part I lost stuff. I now am getting an error saying "A folder was not found. Could not find a part of the path '/tmp/rm/WorkDir/tmp/rmWorkDir/data'.