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Lots of InDesign-generated EPUBs suffer from loads of redundant classes. That may be part of why you’re having limited luck tweaking the css, can happen when you’re adjusting .footnote-class_97 instead of an identical .footnote-class_62. Inheritance/specificity might be a factor too.
The DOCX tip above is definitely worth thinking about. If you can’t just roll back to your source manuscript, you could probably use something like calibre or pandoc to convert the messy EPUB to a new DOCX and rebuild from there. Usually faster/easier than cleaning up an InDesign ePub.
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