Backdriven stepper motor "powering" rest of the board
The voltage coming out of your motor probably is AC, but that is being rectified by the kickback catch diodes in the driver circuit.  Assuming this circuit was designed and wired up correctly, only the correct polarity voltage will be fed back onto the DC power input net.  As long at this voltage doesn't exceed what the circuit is rated to operate at, there should be no problem with this.