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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 commentNicolai commented
Even in 15.1.1, I have exactly the same issue when opening a file that was initially created with an older version. Only when I change text immediately next to the footnote reference does the footnote appear – not when I do any text operation anywhere in the file (as described above by amaarora).
The workaround by Khalid AlAjaji seems to work for me: global search for all superscript characters and change it to the same colour (or some similar “change” with no effect – I suppose the trigger is to do any kind of change to the footnote reference in the text to make the footnote reappear). However, I still wait for the customer’s feedback.
Adobe, THIS IS VERY SERIOUS, please solve this! Sending files to customers with missing footnotes is very bad for my reputation. Please, please, please solve this!