It seems to be hit and miss when converting from PDF to ePub. A lot probably depends on the type of PDF and how the layers are used. I've never really liked any of the conversions I've done, especially if I used calibre.
Sometimes playing around with calibre's Line Unwrapping Factor field on the PDF Input tab helps. However it is certainly non-intuitive to use and requires trial and error--mostly error in my case.
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