I've ditched that book rather than waste hours on the puzzle.
the displayed TOC I was fine in both n ADE & in calibre viewer after I did a toc rebuild in Sigil, & was fine on the Aura HD also.
FWIW the Kobo android app ( with a standard epub imported) works like the kepub renderer on the reader. It clearly opens only one chapter file at a time, because you see a very short " thinking" spinning icon whenever a new long-ish chapter loads, & then the footer data is computed for that chapter + your current screen settings. i.e. the number of pages in the footer is the actual number of screens needed to display that chapter with your current font size choices.
So the only places it can get footer info from is inside that chapter file or in the TOC file, which I guess it also keeps in memory. Possibly it gets it's footer text from the toc & not from the chapter file _ I@d have to deliberately alter the labels in a toc files to test that
I did notice that the android app was consistent in that it messed up both the footer & the relevant TOC entry when you pull down the toc shortcuts via settings ( works differently to the e-readers ) _ you have a pull down tab that does toc & also does the link to annotations. teh software must have some "rle" that sasy flal back to using the html file name if you can't get a proper "chapter title" but it is not at all obvious why it glitched on that one file. all that was "special" about that file was that I did a manual split in sigil because the book had 2 short stories within the same chapter file.
navigation within compilations of short stories can be more problematic than novels, esp. if they are just glued together from different sources. What goes in the Toc could be each story title, or each story title+ author, or both as separate entires, I've seen all of those variants. IT gets messier if some stories are a single chapter but some have chapters of their own...
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