Thank you DNSB. I just realized the ToC-setting command that I'm looking for isn't in the conversion logs for exactly the reason you describe - I update the ToC after conversion. If there's a way to access the editor's logs, that would help.
Otherwise, I'll look into this Xpath suggestion. I'm new to Xpath and epub design, but I'm curious why there are only three levels of command-line flags (--level1-toc,--level2-toc,--level3-toc) when the ToC could be nested deeper than that. Does "level 1/2/3" in those flags refer to the nesting depth of a particular element in the ToC?
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