Originally Posted by PatNY
Sigil does not support toc.ncx files. The TOC is destroyed when you open and save an epub in Sigil that contains such a file. I think the developer is planning to add support for it later.
Another option for your consideration. For simple EPUB tweaking, I find the little free utility discussed/offered on the Atlantis WP blog
quite useful. You can tweak most of the epub constituent parts, including toc.ncx, in-situ using your favourite text editor, without destroying anything.