Hello,
I was incorrect on what you were attempting to do w/ your idea and set up. Maybe setting a reset pin would help. For instance, I use a Cape called the Motor Bridge Cape. Primarily, I use this Cape for testing and fun. I have created a mower that runs in angles until it is done but on this MotorBridge.py library, the idea is that it resets a pin.
I thought using a reset pin may work. Do you think there is a way to use the USB as a reset pin?
Just for kicks, I am replying, e.g. as your method of using the BBB is out of my scope. I am sorry.
Seth
P.S. If you get bored and you think I am on to something, do not hesitate to reply. If not, I understand.