While it is possible to use "save as" when you are in the map window, once you have published a web mapping application the only thing you can do with that application is recongifure it. I would like to use the "save as" feature for one of my applications so I can change one configuration feature and deploy the application. I have all the colors and text the way I want it and all I want to do is deply the map without the edit button button visibile. I don't want to have to go through all the configuraton again just to change one feature and I don't want to share the editable map to anyone outside my organization. Essentially a copy and "paste as" feature would be nice for web mapping applications.