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For epub3 the TOC tools work on the nav. For epub2 they work on the toc.ncx.
So ... You should run the Tool to create/update it manually once before saving your completed epub3 to force the toc.ncx to be in sync with the edited toc information in the nav.
At some point, creating a toc.ncx for epub3 will be the role of an output plugin and not part of the standard epub3. Right now, we have decided to keep it but you must manually rebuild any toc.ncx from the nav if you make changes once before the end.
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