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The best option is to find another version of the book, that is not a pdf file.
If that's not possible the next best option is to use an ocr software to scan the pdf file and convert it to formatted html. ABBYY FineReader is great, but expensive, tesseract is a freeware alternative but not as comfortable.
If you only rely on a calibre conversion, you can use Sigil to manually edit the format of the by calibre created epub and remove empty lines etc.
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