I'm guessing Sigil is not recognizing your chapter headers for its TOC because ID4 is not using <hx> tags, but rather something like <p class="heading-1-with-overrides-2"> (Hopefully all chapter headers of a given level will use the same class)
To fix this, globally replace the <p class="whatever"> tags with <h2 class="whatever"> tags (not forgetting the closing tag!) and then in the CSS, change the p.whatever { ... } element to h2.whatever { ...}
Now Sigil will find your chapter headers and create the toc.ncx.
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