I've added books to my iPad book app via the "Open in books" option while viewing a PDF. To be clear, these are not "books" bought on the Apple Store, they are PDFs which may or may not have ever been a book. Now, when I delete them, they still appear as a choice on the iTunes app when I sync my iPad.
This is similar to Delete book from iBooks Mac when I delete it from iOS with I hope, a couple notable exceptions. Over 5 years have passed, and the process may be different. More important, that question was referring to purchased books. I accept that if I buy a book, I may be stuck owning it forever. In this case, I was using the book app as a repository of PDFs for easy access, but not expecting them to be a permanent addition to the collection. Yes, I understand I can deselect those titles, but am specifically asking for a long term removal.