If all of your section header's footers are linked to previous, then create a new document with the headers/footers you want and copy the entire old document except the last paragraph mark into the new one. That should work.

You may have to create first-page/even-page/odd-page headers and footers for the new document even though it only has one page.
Header/Footer Settings Recap

This will help you analyze your documents:
Word Toolkit for Advanced Management of Word Headers and Footers