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Vmot accidentally shorted to GND, why does this affect the arduino? [RAMPS 1.4]

Posted by JeremySiegfried 
Short and sweet, I made the stupid mistake of trying to replace the X-axis stepper driver while the unit was on, using metal needle-nose pliers. I saw a spark when Vmot was shorted to GND by the pliers, and after that the Y-axis stopped working.
After completing the driver replacement with the PSU off, I then investigated the potential problems that could be the cause of the dysfunctional Y-axis. To my surprise, there was nothing wrong that I could find by testing the pins with a multimeter: Vmot, Vdd, and both GND pins were working, and when I told the printer to move the Y-axis, I got 5V readings from the logic pins (coming from the arduino). I double-checked RAMPS 1.4 schematics for vulnerable components, tested my spare stepper drivers in the X-axis slot, and even swapped the motor connections to confirm that the motor and cable were still working. Nothing seemed out of place.

Until I tested the logic pins, I figured that I somehow managed to kill an IO pin on the arduino (which has happened in the past), and was planning to buy a new one, but now I don't know what needs to be replaced/fixed.

To clarify, this is less of a message to get immediate help, but rather an interesting scenario that I would like to understand better.
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