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don't see how telling it NOT to add chapters will help
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That option tells Calibre not to add *autogenerated* chapters. Thus I hoped by supressing the autogenerated chapters, the original TOC could be preserved...
I can't understand why you have this problem, perhaps it could be connected somehow to the empty h1 tags. But if preserving the EPUB TOC does not work from some reason in this special case, you can still try creating a new TOC - tell Calibre to use h3 tags instead of the default h1+h2 in the Structure detection.