I figured something out and I figured it would be helpful for people to find the solution here in the future.
Essentially I’m the sending a msg.payload = ‘{“MT”:n}\n’ (in Node-RED) to the serial port, and it returns its current value. If the value of MT is not the value I set in the config, I assume that the configuration is off. Thus, reconfigure the Due.
I hope this will help people in the future who run into the same issue.