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There's really nothing you can do about it. PDF is not a "book" format - the file does not contain paragraphs, lines, or even words, but just instructions of the form "draw a letter 'A' at coordinates (x,y) on the page". It is virtually impossible to get a good "conversion" of a PDF to any other format; they will generally require extensive editing after conversion.
"Don't use PDF as a source format" is really the best advise; regard it purely as a "terminal" format.
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