Let’s say someone accidentally deleted an extended Web Application via IIS Manager rather than Central Administration. You’ll find out you’re going to have a bad time. I tried extending said web application using the same name as before and was presented with the error “The IIS Web Site you have selected is in use by SharePoint. You must select another port or hostname.”
To fix this issue you can go to Central Administration > Application Management. Select the Web Application that was extended. Click on the Delete dropdown and select Remove SharePoint from IIS Web Site. In the following window, choose the site you want to delete from the dropdown and under Delete IIS web sites select Yes. This will completely remove the files associated with the extended web application allowing you to extend it again using the same name.