Do not be surprised if your prototype's purpose changes or shifts over the course of the development cycle. Unfortunately, it is a pretty common occurence. This is where some of the pre-planning you've done will come in handy. Understanding the goals and uses of the prototype will help you navigate the shoals of change. Measure the changes you are asked to make by the expressed goals and uses of the system.
Flexibility is also important when it comes to building the prototype itself.
Time constraints usually prevent you from undertaking a normal, orderly development process to build the prototype. You'll probably have to redo work you've already done once, twice, or several times before. This won't make your prototype team happy, but it is an unfortunate fact of life. Conceivably, you may find yourself doing iterative development. You begin with a rough prototype that is a mixture of placeholders and first drafts of functionality or content.