Just a tiny detail - as far as I know, the middle line is redundant (it should work exactly the same without it):
Quote:
Convert - StructureDetection - Detect chapters: //h:h3
Convert - TOC - Level 1 TOCs: //h:h3
Convert - TOC - Force use of auto-generated TOC: checked
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If your suspicion about Sigil-Calibre inconsistency is right then it would certainly be worth opening either a Calibre or a Sigil ticket...