Eureka! I think I finally figured out what problem you are reporting.
I think you are in WD on the Basic Carter Lake Style Web Page Set Up, and you are editing in the Links to Web Pages box, hitting the Update File button, and the changes are not being made in the mywebpagetemplate.txt file. Am I correct? If so I confirm what you are seeing, I can clear that box, hit update and the links are still there.