Thanks all. The Edit TOC is great. I had not used it before.
I did a test and it was the nested div with class="chapter" at the wrong point (spanning the entire chapter" that was causing a problem. That plus classes named chapterHead etc was causing problems with the TOC in the conversion. Teach me to use an html file I hadn't "tweaked" myself. At least I've now learned how to fix this problem!
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