Can I change the config on an aircraft that’s already flying?
Yep. It won't take effect for three days. All the flights you have scheduled with that aircraft when you change the configuration will remain the old configuration, but the new configuration will start right then. You can track these in your Fleet Management pages.
Also note that you don't get any discount or money back from the old configuration. The cost of the config is going to be the cost you have to pay.