Cause for failure after short circuit Step-Down Converter Input
A lot of voltage regulators (switching or linear) do not like a fast discharge of voltage at the input and require extra protection to prevent the output capacitor discharging back through the circuit and causing "mayhem". 

Maybe your prototype board had enough "variance" to hold-up the input voltage for long enough to prevent this problem arising or maybe the prototype chip was a little better than the ones you used for production.

Try putting a fast diode from Vout to Vin so that when the input voltage gets shorted it also discharges the output voltage virtually simultaneously.