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The fix for this issue is now available in the latest update of InDesign – version 16.1
Please update to this version to get the fix. To prevent problem on existing documents and see the footnotes again, you will have to force recompose the stories.
To force recompose stories, you can use the shortcut Command-Option-/ (slash) on Mac or Ctrl-Alt-slash on Windows
An error occurred while saving the commentSlawek commented
I think I found a solution to disappearing footnotes.
The problem occurs when it is not selected 'Restart numbering every:' in the Footnote Options.
If we choose it and select the "Section" option, the footnotes stop disappearing.
This should be done even if the publication consists only of from one section.