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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 commentGraham Nelson commented
We are having serious problems with this bug (I work in academic publishing). Fixing a typo in one chapter of the same InDesign book will sometimes - not often, but sometimes - cause footnotes to vanish in some subsequent chapters, without any warning. Going to the page of a missing footnote and adjusting the size of the frame very slightly (even if it is then adjusted back again) makes the footnote jump back into existence. But you have to know that it's missing in order to do this, and there is no indication except that if you look on the page, it isn't there. This may happen on, e.g., only four random footnotes out of a 1000 in a book. But four is enough. And next time, it will be a different four. Text silently reflows to fill the space given up by the missing footnote, so the error doesn't only affect the pages where footnotes are missing: it also affects subsequent ones.
All of this makes it difficult to send a revise of a proof to an author without rechecking every page by hand whenever anything is changed anywhere. Indexing is especially difficult.
If Photoshop had been randomly omitting chunks of images since October, I kind of think Adobe would have fixed this by now. They really need to appreciate how serious this bug is. I appreciate that all users believe that the bug affecting them is the only important one. But still, no possible new feature in InDesign would be as helpful to us as fixing this bug would be.