I would goto https://sync.opera.com/web/ and reset your sync data to wipe out all your synced data to start over. I'd also start with a new profile in Opera. Close down Opera and delete the profile folder. See the URL opera://about for the path. Then, start Opera, enable/log into sync, set what you want synced and then use Opera. Then things should work as long as nothing outside Opera is interfering.
I've managed to delete these links. It's "easy" just disable sync, close opera, open history file in sqlLite browser, search and delete the links from "url", and "segments" tables, then save. The deleted urls are deleted even more