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I must admit I wasn't aware that footnotes displayed like that in the viewer but I have just looked at a book I assembled with endnotes in and when there are two footnotes on a page and the first is selected I have also noted that in some (but not all) cases later endnotes also appear but without the endnote number/ backlink.
I haven't seen an example of the invisible italics.
However when I view the book with the Adobe Reader everything looks fine.
Have you checked the book with Adobe or a viewer on an actual Ebook reader ?
BobC
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