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Originally Posted by Bluebird
every page or two has a number or the book title inserted or both.
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That's because the book you start with has that in it. You need to select the remove header or remove footer option. Then you need to put the correct code into that option so that it works for the book you are converting. There is a wizard there to help you, but it's still not easy.
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I don't know why half of the ebooks convert without a problem and others don't?
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Because the books are different. You'll need to either live with the header footer in the text, or remove it for those books that have it, but different books will require different techniques to get rid of it. Searching here for "header" or "footer" may help. Eventually, there will be a new pdf converter engine that will help with pdfs, but it won't be tomorrow.