If you want to change the Root of an existing Chord, follow the steps for Adding a Chord, except for: Name the Chord, as it is already named.
The chord names are saved in a file called PPalette.CHD, and the Roots are saved in a file called PPalette2.SCL. These files should be in the same directory in which you installed the software. It is a good idea to make a backup copy of these files if you are going to experiment.