Well, what was I going to do?
I tried to recover what was left. Many folders and files were just randomly spread across the Opera link directory where I at first couldn't find them, instead of deleted.
Then I tried to ease, but online editing is hardly possible. Trying to sync really deleted most of the bookmarks this time. At least there wasn't as much to sift through.
So I put everything in the trash and picked out the good stuff, put it into new folder and basically started over. Now I will backup my bookmarks and pray this won't happen again.
You really need to work on that sync code, guys at Opera!