You swapped the connections to the controller and suddenly it started working again. What you changed was the physical position of the connectors either at the motors or at the controller board. The Y axis cable connector was probably not making proper contact with either the motor or the controller board. If it was the driver, the problem would continue (busted ICs don't spontaneously fix themselves). Motors almost never fail. That leaves the cables/connectors as the most likely (99.999%) culprit.
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