iBooks does not actually change PDF metadata at all. It may appear to allow you to edit metadata, but the PDFs actually retain their original file names and metadata attributes even after you painstaking edit them. You've essentially wasted your time, as did I. Furthermore, you may notice the utter mess that appears in your Preview folder on iCloud Drive. Some PDFs may appear with "in iBooks" under the file names, while others do not, still other PDFs may show up in there that you may have sent or received via email, but never formally added to iBooks. The greatest failure, and iBooks is an epic failure, is that the second you are tempted to organize your "Preview" folder on iCloud Drive, it will likely break iCloud sync of iBooks and PDFs across devices. If you are OCD, like me, you will find yourself in an endless feedback loop of fixing ugly metadata and organizing reappearing and disappearing PDFs. You would be better served to stop using iBooks until they fix it, especially if you wish to stay sane.