To be able to change Port settings in the Motion Architect terminal, the terminal needs to be disconnected. The default state of the terminal when you open it is for it to be connected.
After opening the terminal, select the Transfers menu and select Connect. If there was a checkmark next to Connect, this will disconnect the terminal. If there was no checkmark, then this will connect the terminal.
Once the terminal is disconnected, the settings can be changed under the Settings menu. Be sure to reconnect after changing the serial port.