[chaley]

Originally Posted by theducks

I believe if you IMPORT a Index.html with the file names in the proper order.
See this section in the help files http://manual.calibre-ebook.com/faq.html#id19

And in particular look at the note in that FAQ section

Note

By default, when adding HTML files, calibre follows links in the files in depth first order. This means that if file A.html links to B.html and C.html and D.html, but B.html also links to D.html, then the files will be in the order A.html, B.html, D.html, C.html. If instead you want the order to be A.html, B.html, C.html, D.html then you must tell calibre to add your files in breadth first order. Do this by going to Preferences->Plugins and customizing the HTML to ZIP plugin.

If the order in the TOC is correct and complete, and if the chapters contain links to other chapters, then you almost certainly want to change to "breadth first".