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@mlamb
The NCX is king in the Sigil automated chain.
Note the Pulldown choices in the lower Left corner of the (ncx) TOC creation tool. Those may simplify things. Also note that you can style more than 1 header class to look exactly the same
You can try a 2 pass approach.
Remove all class="sigil_not_in_toc" in any header you want in the SUPER SET (html TOC) IF NEEDED (this puts the ticks for that item back again in the NCX TOC generator)
Generate the (ncx) TOC for the super set values
Now use Sigils Generate HTML TOC
You now have the the super set Inline TOC. Note: Sigil does not number TOC items, it just indents if at differing levels
Now rebuild the NCX to the smaller set (the level filter may work for you) by removing the ticks to hide the item
The HTML TOC has its own stylesheet, that can be customized to your hearts content
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