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You can run Generate Table of Contents at any time and it will always replace th current ncx. But before doing that you might try to running the TOCSaver plugin before trying to generate a new table of contents as it may help prevent loss of some post edited heading titles.
Does the current NCX have a pagelist section if you look directly at the NCX? I can't see how any pages can be assigned without it? Could your epub be using an adobe pagemap.xml?
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