@lei261 you are vary lucky not to have damaged anything. Typically, excess voltage applied to the 5V rail damages the 3.3V regulator and quite often the microcontroller and network module too. In your case the A4988 chip appears to have shorted out the 5V rail before more damage was done.
BTW Duet 3 boards (except for the Tool Board) are protected against this type of short, however other devices connected to 5V such as PanelDue are not protected and would still be likely to suffer damage.