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@Rune: You will probably need some code beyond the standard export options. What DTD are you trying to export the XML with?
I know more than you will ever want to know about JATS xml. The EPUB output would depend a lot on what the specific JATS tagging is. Using InDesign as an intermediary to achieve the EPUB from JATS is not all that helpful unless you are making the print pub layout with the JATS XMl also. Do diligent research on the JATSKit which includes an EPUB output feature.
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