If you change the configuration name in the design table, it will create the new configuration, but also keep the old configuration. However, the old configuration is no longer controlled by the design table. Also, the problem with this is that if there are assemblies that are using thousands of these parts, you have to edit each instance in the assembly to use the new configuration number. 

In contrast, if you just change the configuration number outside of the design table, the links are automatically updated. Has anyone out there run into this before, and if so, what is the best practice for changing configuration names driven by a design table and have the design table, and any assembly that this part is in, update accordingly.