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PDF afaik has practically zero semantics and relies instead on arbitrary layout, or at the very least most don’t use any sort of semantics. EPUB on the other hand relies heavily on semantics and organization. You will be very well served to roll back to whatever made the PDF rather than the PDF, and if that’s not available probably knuckling down and just reading the PDF instead of trying to convert it. Thinking of sidebars in particular is giving me a deep malaise.
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