Another thing you can do is to test bookmark changes in a test standalone installation of Opera. Don't enable Sync. Just check if changes stick. The changes will probably stick no problem.
If so, that could mean there's something messed up with your files for your regular Opera (due to Sync corrupting things or due to corruption for some other reason or due to write permissions on the files). If that's the case, it might not be something Opera can fix itself via an update or anything.
If that's the case, you would have to fix it yourself by turning off Sync, going to https://www.sync.opera.com/ and choosing "reset passphrase" to wipe out all your sync data, closing Opera and renaming your user data and cache folders to start all over from scratch.
If you were to do that, you could goto the URL opera://bookmarks and use the drop-down at the bottom left to export your bookmarks to an HTML file. Then, with Opera is all fresh, you could goto the URL opera://settings/importData, choose "Bookmarks HTML file" in the drop-down and import that HTML file. Then, you could goto the URL opera://bookmarks and organize your bookmarks (as imported bookmarks will be on the bookmarks bar). Then, if you wanted to use Sync to sync your bookmarks, you could log in and sync your bookmarks and test if everything is fine.
(Doesn't sound like you'd have to export and import your passwords or anything else though as it looks like you clear those each time before you close Opera. But, if there was anything else you wanted backed up, you'd have to do that first (if possible).)
Doing all that would be the only way to be sure everything is correct and not corrupted.