I managed to figure it out.
basically you add this code to the end of the last xhtml doc:
Then in the toc.xhtml file the list element would look like this:
<li id="ID" class="CSSCLASS"><a href="Text/Chapter_01.xhtml#com_apple_itunes_epub_end0001">Section not in the sample</a></li>
For each entry in the TOC that you want greyed out, you add a new anchor tag and link to that tag.
And the reason that we make our own samples is that we are a music publishing company and we want control over what we give away.