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There is no concept of a 'paragraph' in pdfs.
PDF unwrap works based off of punctuation, html that pdftohtml generates doesn't provide any other clues as to what is and is not a paragraph. You just need to fix it up yourself after conversion unfortunately.
There is a new pdf engine that will probably get released someday which contains info such as indentation and spacing between lines, which could be used to determine paragraph boundaries. No telling when it will be ready though.
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