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@mrevent: If you used my plugin to put all your footnotes in one xhtml section then you can use the plugin to remove the xhtml section containing all the footnotes and then use it to put footnotes in each xhtml file as follows:
1. Run the plugin. Ensure that all the settings are the same as when you built the footnote section.
2. Click Reinstate footnotes. This removes the section that contains all the footnotes from the ePub.
3. Run the plugin again and make sure you have selected the option Current xhtml section
4. Click Insert footnotes to insert the footnotes in each xhtml file.
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