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PDF does not necessarily have a concept of indentation. Text (every line, or every word, or even every letter) is positioned using x,y coordinates on a page. Visually this is fine as you as a human recognize it, but it's a nightmare when it comes to machine-readability.
Enable the Debug feature in Calibre conversion and check the HTML of the first step (input html). If that is properly indented or at least has any kind of indication of indentation or different formatting for indented lines, then you might be able to convert it by using a HTML editor on the input file and search&replace those indicators. That's what I did with my last PDF file and it worked well.
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