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Sorry I did not explain very well.
The problem with turning a PDF into an ePub is that no software is smart enough to understand the PDF. Sometimes there are images, sometimes some text in sidebars and sometimes headers and footers. Not to mention the line breaks and tabular data. Rarely I come across a PDF with none of these problems and then I just turn it into an ePub (with or without the custom css). In most OTHER cases, reflowing in the reader allows me to read the text. And when something (e.g. a table) does not make sense, I go back to page view (PDF) mode and look at it that way. Then I either zoom in to read text or reflow again to read it. This flexibility is not there if I turn the PDF into an ePub beforehand. Then I am stuck with the messed up tables and sidebars.
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