Many users have been wondering why their PDF files still exist and are not deleted after being moved completely to another category in iBooks on iPhone or iPad.
This issue really annoys people who DO NOT want to have duplicate PDF files in different categories. And some people might face a serious problem that if they attempt to delete the original file from the old category, the second one will be removed completely in the new category.
Why? Because you have not upgraded to iOS 8.4 or later version. Upgrade your iOS, you fix the problem.