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Did you try getting rid of those pointless ncx entries?
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Maybe they are referring to ncx playorder numbers not being sequential anymore because you edited the ncx?
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During the iterations seeking to understand the problem, D2D Support confirmed they too had checked the contents and all links in the contents went to the correct destinations. They did suggest that maybe my use of links to sub-sections (it's a non-fiction book) meant that in some cases two destinations might appear on the same page at same time. Of course that depends on the reading device and the font size selected by the reader. But, just in case, I removed all the sub-section links in the ncx Table of Contents (while retaining them in the html contents for the readers' convenience).
After editing the ncx contents with Sigil's tools [Tools>Table of Contents>Edit] and swapping around the order of a couple of smaller files, I checked out the toc.ncx file and Sigil had correctly reordered everything and the playorder was correct.
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Maybe D2D has updated their intake app to add synthetic page numbers if no print page numbers are present? You might want to ask D2D about it.
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I always download a proof copy from D2D and I have never seen any alterations made by them. As far as I can tell, the downloaded proof is identical to the copy I uploaded.
From the supplementary info supplied by Support and presented as emanating from Apple after the third attempt, it appears that Apple's on-boarding app derives some sort of expectation from the EPUB file about the page number it expects from the file's table of contents and then finds that this differs from what their app reports when it gets to that page.
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For example, Chapter 13 has page 159 listed in the Table of Contents but it is on page 160 in the book.
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I've tried reading this epub file in several readers including Calibre's reader, Kindle's Previewer3 and Adobe Digital Editions (which is D2D's recommended app). I never saw any problem - or page numbers come to that. I'll try and get confirmation from D2D that they have made no modification to the file before they sent it to Apple.
Could I maybe generate a new ncx table of contents from Tools > Table of Contents > Generate? Is there a preferred procedure for so doing - deleting the toc.ncx for example?