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If that doesn't fix it, then it is more than likely being caused by one of the other ERRORS being reported. Always fix errors before worrying about warnings.
One of your actual errors is about a filename in a reference element not being manifested. I'd wager if you got that fixed, your warning would go away. That reference item (found in the guide section of the OPF where an html toc would be) is very likely your html toc. Imagine what might occur if your html toc (correctly tagged with the toc semantic and everything) were that unmanifested file?
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