I dont know about modify epub, but Polishing should work fine with epub 3, if it does not you can always restore the original file after polishing, and let me know what the problem was.
EDIT: The only problem I know about is that updating metadata will not update the epub 3 specific metadata fields, which practically speaking, means the epub 3 series field.
Last edited by kovidgoyal; 05-13-2015 at 06:29 AM.
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