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You say you need to create an html toc, yet you describe an NCX file. Also ... simply adding new navpoints to the NCX file is not going generate those errors in html files. You're confused about something and as a consequence, are not supplying enough info for anyone to really be able to help you.
At a guess, I'd say you have links in Section0004.xhtml that are pointing to ids/anchors that simply don't exist in Section0001.xhtml.
There's a link in Section0004.xhtml that has an href that ends in Section0001.xhtml#footnote-4083-10, but there is no element in Section0001.xhtml that has an id of footnote-4083-10. Ditto for footnote-4083-11.
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