I had a Pixhawk connected via the official power module, itself supplied by 12V from an SBEC itself connected to a 36V battery supply. 

I say had, because the SBEC failed in a cloud of smoke and now neither the Pixhawk, nor any of its ancillaries work any more. I am 99% sure that the damage is unrecoverable, but I am more interested in how to protect against this kind of issue in future. The Pixhawk is completely dead (no LED's) and measuring the voltage across the FMU power led I get around 0.4V when I think I should get 3.3v.

I presume that what happened was the SBEC failed short and so supplying 36V direct to Pixhawk's power module and hence Pixhawk itself. Is there an easy or sensible way to protect against this sort of thing, other than buying a higher capacity power module instead of the SBEC arrangement?

I should say that in this setup, the SBEC also powered the servo rail and a water cooling pump.

The SBEC was a Turnigy Multistar 6-50V with twin 12v and 5v outputs. Upon disassembly, I am not enamoured with the design of this SBEC and would be interested to know if anyone else has had problems with these when operated easily within design limits (rated for 15A and was protected with a 10A fuse upstream which didn't blow). 

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To prevent too high voltage from a defective step-down switching regulator, you can connect a ~2A polyfuse, then a powerful zener ~6v zener.

Should the voltage go above 6v (, the zener will short, and trip the polyfuse)

be sure to use a powerful zener, or a transistor + zener to do the shorting. 

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