Since the new Microsoft Edge is Chromium-based like Opera, you could goto the URL opera://about in Opera and the URL edge://version in Edge to see where the profile folders are at. You can then close down both browsers, delete all off Edge's profile files and folders and replace them with Opera's to see what happens. You might get luck where Edge accepts just about everything. Test with a copy of your Opera profile just in case Edge ruins it. If it doesn't work out, just delete Edge's profile folder so you can start with a fresh one.
No guarantees that will work. Edge is Chromium-based like Opera, but Edge could do some things differently enough to make the profiles incompatible.
@cratte I use several browsers. Opera is currently my default but I was along-time Firefox user. At this point Firefox's auto-complete is still superior to all competitors. It's difficult to explain but basically everyone needs to copy Firefox! It is one of the key features that kept me glued to Firefox for years.
Opera's implementation is not too bad but still not as good as Firefox's. but now the other features of Opera have tipped the balance, hence why Opera is now my default.
Opera Sync has an engine to delete duplicates, but don't know its rules and efficiency.
Try SuperSorter from Chrome Store and take care when deleting, keep a BackUp, even from the messed BK.file.
Windows 7 (x64)
Opera Test profile | Opera Back up | Reset
Thank you. I can't believe I haven't thought of that and it turns out the solution was that easy. It will take me some time to take the bookmarks out of folders they were thrown into, but at least I have them in browser now.