The only thing that I could recommend is to export your bookmarks regularly in the future, so you can restore them from there or transfer them to another device.
Sorry, I don't have any better solution by now, but I'd like to support your request because I have had similar problems on various occasions:
when synchronizing, it went the wrong way: it did not update the stored bookmarks with the new ones but removed the new bookmarks on the computer, so the former version was restored on it (although adjusted the "right way" round in Settings).
It happened too many times so I don´t consider synchronizing a safe process on Opera. It might function sometimes but I think it´s better to have your bookmarks exported and stored.