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If you're using Calibre to convert pdf to epub, another option is to try changing the "line unwrapping factor" for this pdf. You will find it under Calibre's Convert - PDFInput - Line Unwrapping Factor. It is used to try and determine how to reconstitute paragraphs from the pdf's individual lines.
I can't tell you what value to use because the 'best' value depends on the particular pdf. It is a number between zero and one. The default is 0.5, so try 0.6 and/or 0.4 and experiment until you get a better-looking epub.
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