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PDF conversion is always a bit hit-or-miss because PDF files do not internally have the concept of sentences, paragraphs even words!
You probably need to play with the line unwrap setting in the PDF conversion settings. This can help with deciding when a new line is a new paragraph or merely a continuation of a previous one. The problem is that setting it too low or too high can also have undesirable side-effects so extermination is necessary.
You might also find that enabling heuristic processing (which I think will try and guess at a good setting for line unwrap amongst other things) will improve the results. Again it is a case of try it and see I am afraid as it helps with some books but makes others even worse.
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