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
78 votes12 comments · Adobe InDesign: Bugs » ePub/HTML/Publish Online · Flag idea as inappropriate… · Admin →
Thanks for reporting the issue.
We will review it shortly
214 votes50 comments · Adobe InDesign: Feature Requests » Text and Type · Flag idea as inappropriate… · Admin →
Thank you for your patience all this while.
This issue is now fixed in the latest update (Id 14.0.1) of InDesign CC.
If you are unable to see the update notification yet, open the menu (three dots) from the top-right of Creative Cloud desktop application and click on ‘Check For App Updates’.
Once the update button is shown against InDesign CC, click on the button to update your InDesign to Id 14.0.1 for the fix of the issue.
Do let us know in the comments, if you face any problem with the new update.
List of fixed issues can be found at: helpx.adobe.com/indesign/kb/fixed-issues.html
An error occurred while saving the commentAnonymous commented
Also I am still having this problem with Adobe InDesign version 14.0.2.