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I think the trouble is that the file toc.xhtml serves double duty as the nav file and as the visible table of contents.
I can fix that by making a copy of the file. That copy is then unaffected by a recreation of the toc and retains its formatting.
The trouble with that particular epub3 is that there are lots of links to the original toc.xhtml which all get broken as soon as I edit the toc via the menu because all the ids are lost.
Also, there is a toc.ncx file in addition to the toc.xhtml "nav" file. I'm not sure what that's about. I thought the ncx file is for epub2 only?
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