You definitely can change domains added as a project anytime. It’s entirely up to you. What you can’t do is add two projects with the same domain.
To change the site in a project, if you already used all your projects, you will first have to remove one. You can learn how to remove a project here.
Once you have removed the project, you’ll then be able to add a new website you would like to. Notice that removing a project means you will lose all the historical data collected while that website was on your Dashboard.