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PDF conversions to ePUB are not easy. They require much manual effort. Usually the best results are achieved when performing OCR on the PDF.
If the PDF contains images, it gets even worse.
My advice is to either read the PDF on the Nook (I do not know if the Nook supports PDF) or convert it in total and be prepared to loose all formatting by default. You need to reapply the formatting later if you can.
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