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If an epub3, just generate the ncx from the nav (assuming the nav is correct) using the epub3 tools menu.
If epub2, use save-as to save your current epub under a new name in case anything breaks. Then try rebuilding the ncx toc (not the html toc) using Sigil's toc generation tools. This should work to fix your ncx as long as you use proper heading tags throughout your xhtml pages.
If you did not use headings properly, then hand editing the ncx code may be your own,y approach.
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