I just ran a manual scan (same options as on the profile page) and it removed the game, not sure why it didn't when you ran it. I'll add some logging to see what's going on there in the future, functionally there should be no difference from the scans I run and the user option.
PSN hidden games are auto removed as well, though we don't check for it that often (about once a week), since it's not something that can be detected through incremental scans.
@CoWarZz I will consider it. At least for PSN it's not really necessary though.