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Run a conversion from PDF to epub with debugging turned on and then look at the intermediate HTML output (conversion goes something like PDF -> very rough HTML -> cleaned up HTML -> epub). Looking at the cleaned up HTML step should help you figure out how to find chapter breaks.
Or you could even take the intermediate HTML, modify it yourself to make chapters <h1> or <h2> elements, load the HTML into calibre, and convert to epub from the HTML rather than PDF.
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