I had the same thing happen, all folders gone. But I also got a bunch of errors and had to restore from backup like 4 or 5 times before it worked, so that may be related.
In the past I had this happen more than once, in my case I had several folders named "Games", never got an error, they just got all screwed up, position, contents, etc.
I started naming them "Games 1", etc, and now they restore fine.