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You need to look in your content.opf for the spine tag. It will have itemref child tags. Each one points to a manifest id for that entry and each one allows a linear= attribute.
So take a screen shot of the opf spine. Then look in the opf manifest to find which file that refers to.
To make things simpler, you can pm me directly for privacy reasons with screenshots of the opf spine (entire thing not just the opening tag) and screenshots of the opf manifest (again entire thing), I can point out what to do. Similarly you could just pm me the content.opf file instead.
It is a minor change. You have done nothing wrong, Many epub devs add a user oriented table of contents xhtml independent of the nav itself. Mainly at the end. And Sigil supports that by default.
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