Working with AFP/SMB on your QNAP and different users and/or operating systems can mess up your file permissions. The reason therefore is pretty complicated - but the solution to fix it is much easier.
So if you ever tried to delete a file and it was not possible, or a file was hidden instead of normal viewable - but all of that should work - this trick could help you. Login to your QNAP using SSH and use
set_volume_mode _name_of_share_ ex.: set_volume_mode Qmultimedia
All problems solved, permissions on the file system itself are corrected and you can go on with your work :)