Hello everyone! I'm having this same problem since yesterday.
I upgraded the browser on my main machine to version 62.0.3331.72, and upon completion I was greeted with a virtually empty speed dial: of the 20+ folders I had, only one appears, with less than 5 entries on it. I looked everywhere I could, even in the bookmarks trash, but those folders practically vanished. To my comfort, all my other speed dials and bookmarks appear intact; but they all reflect this machine's "barren" status, including the Opera Sync page.
Thankfully, I have a secondary Ubuntu machine that hasn't synced yet, so I imagine a copy of my old speed dial should be there. Regardless, I'd rather wait for an official pronunciation on this issue before trying to restore anything to this machine.