Originally Posted by BakerBug
4. Remove the PDF from Calibre. (Ops.. this removes the Mobi book too).
It's great that you could replicate the exact sequence and that kiwidude could correct it so quickly.
Just a FYI removing the PDF from calibre does NOT remove the Mobi too. Removing the book removes the book (all files). To remove just the PDF go to the edit metadata window and select the PDF in the available formats window and click the recycle icon. Or you can select multiple books and use the remove format option in the bulk metadata window.