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How did you ever figure this out? I will give this a try when I get some time, but I hate to think of redoing all my epubs, especially the directory structure. The change in the directory structure seems to be important, as all of my footnotes already have the <a></a> tags as the innermost tags, and they are definitely not showing as popups. My stylesheets are located in OEBPS/Styles (instead of OEBPS/ as you show in your attachment), so if that's the main problem, it might be an easy fix for Kobo to implement. I hope, I hope, I hope. Thank you for posting this.
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