[KevinH]

Go to Sigil Tools menu and from it select the Epub3 Tools menu. These are the epub3 specific tools to delete the guide and ncx. There is another tool there to recreate the guide and ncx based in the current nav. So no need to manually edit the ncx. There are also tools to update Manifest properties.

So once you are happy with the nav, use the epub3 tools to delete the guide and ncx, then the epub3 tool to create the guide and ncx based in your nav so that they match.

Then as a last step, run the Update Manifest properties tool just to be safe.