There are/can be 2 TOC in EPUB2
The required 1 is the NCX. Calibre TOC edit (it is also available as a GUI icon ) works on this.
If you used the 'inline' one (in the book), you will need to regenerate after EVERY TOC edit (session) as this as it uses the NCX for for the current links. THIS CAN ONLY be done from the TOOLS: Table of Contents MENU
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