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The toc.ncx is technically not to be used in epub3 and need not be present. Epub3 readers should always ignore it in favour of the nav. Sigil supports including a toc.ncx in an epub3 so that older epub2 based readers can still be used to read the epub3. If making an epub3, wait until you have fully edited the nav and then use the simple tool for epub3 we provide to sync the toc.ncx to the nav. You also should rebuild the manifest properties just to be safe.
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