During Autoset Chapter LZ, the FOOTNOTES: landing zones are placed at the top of the following chapters title page instead of at the bottom of the last page of the chapter the footnotes belong to, e.g.
Footnotes Chapter ends new page New chapter title
becomes
Chapter ends new page FOOTNOTES: New chapter title
instead of
Chapter ends FOOTNOTES: new page New chapter title
Thus the table contents and index references no longer link to the chapter title pages. Instead they link to the beginning of the footnotes from the previous chapter.
Steps:
Anonymous
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You forgot to include a demo file. Running the steps you describe on an empty file doesn't show anything (unsurprisingly). I couldn't replicate on a random file.
Remember that steps to replicate isn't about explaining which menus to use, it's about explaining carefully and with as much detail as possible which steps someone else should take to replicate the problem you're seeing.
Sorry. Here's a demo file with the associated .bin.
Once Autoset Chapter LZ is selected then page through the file and note where the FOOTNOTES: are positioned. In every case they are at the top of the page of the following chapter instead of at the bottom of the last page of the chapter they belong to. The error isn't obvious in the .txt file but inspect the page label assigned to the current page displayed in the bar at the bottom of the page. The page number is supplied by the information from the %::pagenumbers = ( section in the associated .bin file. Apparently the offsets point to the FOOTNOTES: line instead of the following line.
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I can confirm the problem on the supplied file. The footnotes in the file need some cleanup, but that's unlikely to have an impact (still most projects would require a clean and smaller demo file).