Running a conversion on it will build the TOC from scratch. There was also a TOC editor added to calibre in recent weeks. I haven't played with it much, but it has options to generate the TOC from headings and other things
You could also use epubcheck to validate it or open it in Sigil to check it. Sigil also has options to rebuild the TOC.
And I'm always interested in seeing what causes these problems. Any chance of sending me the book to look at? If so, PM me with a download link or an email to send it to.
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