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Originally Posted by tartanpion
Ok I have merged the part45.html and generated a new toc for files with calibre editor and all the footnotes seem to have the same pop-up behavior. I don't have see anywhere that the toc could disturb the footnote/endnote with kepub.
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@DNSB gave you a link to the closest thing that Kobo publishes as specs for kepubs. The book didn't meet those specs. Therefore, you cannot assume anything will work properly.
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Can this be "automatized" with the plugin ?
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You can have the conversion either split the internal files at different spots, or, generate a the ToC in a different way. You would need to look at the book to decide which is best. My quick and dirty test was to use the editor to remove the current ToC and generate one for each file in the book. An alternative would have been to generate the ToC for the h2 tags. Though I don't know if that would have gotten everything.