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Not sure what your issue is with section breaks as the review was removed, but it might be worth pointing out that the freebie MobiPocket Reader for PC often does a far better job of converting PDFs, Word, HTML and plain text than Calibre. It's a drag and drop affair too, and you can then run the resulting PRC file through Calbre to get a MOBI (they are essentially the same format) with no loss -- which you need to do if you have made any changes to the metadata and you want them to stick.
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