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The only reason to add an NCX to an epub3, is to help support ancient epub2 only e-readers. Under the Sigil Tools menu under epub3 tools is a tool to create an NCX from the epub3 nav. It will sync them.
You will need to hand edit the actual epub3 nav document. Following the pattern of the existing li tags inserting a link to the new file.
Once that is done, you can use the epub3 only tool to create/update the ncx fromthe nav if you want to support those older epub2 only e-readers.
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