Extended web applications are not listed in the web application list and cannot be deleted using the Delete Web Application link in Central Administration.

Use the following steps to delete extended web applications:

1. Start Central Administration
2. Go to Application Management
3. Click Remove SharePoint from IIS Web Site to get a page with a form similar to the following.
   
4. Select the web application that the extended web app was extended from
5. Select which extention/zone to delete
6. Select whether to keep or delete the IIS Web site
7. Finally click OK