It looks like the App Note was based on a different derivative MCU than what you're using. Look for headers for your MCU derivative in your project. These are usually lurking in the Libraries folder in the CodeWarrior project window. Now modify the old header file references in the source code to point to the MCU-specific header files that your project uses. (That is, modify mc9s12dp256.h to be, say, mc9s12dp512.h.)
Alternatively, you can make a new basic project with the CodeWarrior wizard, then drag and drop the source files from the App note project into the Project window of the new project.
---Tom