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When the input document has a Table of Contents in its metadata, calibre will just use that.
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I assumed that the TOC entries that Sigil shows in the TOC editor are metadata based. There are not any TOC pages with hyperlinks in the epubs.
Most epubs were edited in Word, saved as Filtered Html. All chapter titles have H1/H2 sytles. No TOC is added in Word. From there, copied/pasted into OO Writer and converted to epub. Double checking in Sigil shows all formatting to be fine and TOC entries are all there. Conversion in Calibre without using Force TOC will sometimes produce epubs with "Start" as the only TOC entry.