Quote:
Originally Posted by tbrosz
Which specific box did you click on the "Generate TOC" commands?
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I think you're over-complicating it

If you open the TOC of the epub3-with-no-NCX with the calibre TOC Editor then you don't need to 'Generate' anything. Just immediately re-save it by pressing the 'OK' button. Calibre will auto-magically create an NCX which matches the NAV and do any necessary housekeeping (e.g. OPF update).