I pasturize my cider to kill the yeast so I can back sweeten it. Just heat it up to 160 or so and then put it in a keg and cool it back down. Put the gas to it and it will be carbonated.
While I personally have not and probably will not experiment with Flash Pastuerization, I would give what Spurtrax said a try. However just in case shit hits the fan only try this on maybe 5 or so bottles so your whole batch isn't ruined. Make sure to compare these bottles to the non-pasteurized bottles to see how they taste and how well they age.
According to research that Cornell University did with cider, they had the best results with getting the cider to 155 - 160 degrees and holding it there for 6 seconds. In their case they were attempting to kill off e. coli and they were 99.9% successful. The tricky part seemed to be getting the liquid to 155-160 really quick and then quickly getting it back down to room temp in an immediate fashion. The longer it took to transition from these phases the more likely they noticed a degradation in their cider.
I can't really tell you how much this translates to beer but let us know how your experiment turns out.