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I have found that Flight Crew overlooks empty hyperlinks, and that many of my e-books contain two or three of these. As I recall, they look something like this: <a href="whatever"></a>. I have no idea where these come from, but they suffice to kick out an error in epubcheck (though not in Flight Crew) and to cause the epub to be rejected on the KDP and on the iBookstore. So I always run the file through epubcheck after making my peace with Flight Crew.
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