I am using SharePoint Server 2007 Enterprise with Windows Server 2008 Enterprise, and I am using publishing portal template. I have created a web application for intranet zone. I want to know how to change the port number of the web application? Could I change it directly in IIS manager (is this way safe)?
Deleting IIS site will make you loose all your customizations including web.config changes. So Don't do it!
There is an easiest way to change SharePoint Web Application Port by updating IIS bindings and Alternate Access Mappings. Find the detailed instructions here: How to Change Sharepoint Web Application Port