I was in the process of migrating a MOSS publishing site to a production server. I extended the site to intranet zone to have the default zone to be configured for FBA authentication. While extending the site I made a typo while specifying a host header for the site. When I tried to delete the extended web application by selecting it from the web applications list in CA I was not able to find the extended application’s entry. Then I googled for a while to find a solution and found it here – http://sharepointnotes.wordpress.com/2008/07/17/quick-tip-delete-extended-web-application/.
To delete an extended web application,
1. Go to Central Administration -> Application Management -> Remove SharePoint from IIS Web Site
2. Select the original web application from the list
3. Select the appropriate extended application to delete
4. Press OK