The portal layout information is stored in a database. If you downloaded and are using the portal+jbossas bundle, the database is Hypersonic.
You can use the Management Portlet (log in as admin and go to the admin portal) to remove the older portlet, instance and window.
Or you can wipe out the database (if you are using Hypersonic) by removing the server/xxx/data directory.
I realized that management from admin portal is not enough. It was good to remove unused pages, but when I removed page of mine application and put again WAR with new name empty page occured.
Second solution was better. After wipping database I can do what I wanted. There of course are side-effects: some jBoss errors on console, but pages are shown.