ieee488:
Never connect stepper motor to your Arduino.If I had to bet money, your Nano is bricked.
Read the spec on much current it can source on 5V. It isn't enough for a stepper motor.
Did you even read the question? I was using the board to generate square waves to drive a stepper driver and an external 60 watt supply but that's besides the point, the main problem is the serial line which means I can't reprogram the board, the code that's already on it works perfectly fine