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I could construct a PDF file in a way that made it appear normally in a PDF viewer or print, but have the text come out all backwards when you try calibre or reflow conversion techniques... that's just PDF for you, the format does not care much about actual text structure.
If these errors appear to be random, there's little you can do other than manually fix these occurences. If there's a pattern to these errors, with some programming skills it may be possible to devise a workaround for the particular document.
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