This is an old thread, but I have a working solution - so hope this helps someone ...
- DO NOT CONNECT DEVICE (e.g. iPad) TO COMPUTER
- Start iTunes - I am using latest 12.4.1.6 on Windows 7
- Just under the System Menu, if it shows Music, click on it for dropdown menu, then select Books
- If Books is not listed, click on Edit Menu... and tick the Books item, click Done, then select Books
- Under Library, click on Books or PDFs, then on right-hand side select one or more books, right-click and Delete
DS