Same problem here! I updated to iCloud Drive because I had shared a file earlier with a friend and she couldn't open it otherwise. While I was editing it, I suddenly received a notification that it had been deleted in another location. My friend couldn't open the document from the link, and all my files on all my devices and on iCloud had been deleted! We had been working for so long and had something really hooking and good, too!
I talked to the people at the nearest apple store because I really needed the document, and they told me that when I upgraded to drive, the old documents should be on the normal iCloud because that and Drive are two very different things. However, I tried to get the documents from other devices that hadn't switched to drive yet. That didn't work. Dang.
I am using a Windows, so I can't do anything with Time machine or ~/library/ or anything. Sheesh.