B747-200 FL390 ENRTE NRT. SO BALANCING FUEL. DISTR BY CAPT LEAVING COCKPIT TURNED OFF #3 FUEL BOOST PUMP WITH THE XFEED CLOSED RESULTING IN FLAMEOUT OF #3 ENG. ATTEMPTED RELIGHT BUT REQUESTED CLRNC TO DSND AND HAD A SUCCESSFUL RELIGHT AT FL250. LANDED NORMAL NRT.

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THE #3 ENG FLAMED OUT AT FL390 IN CLR AIR AND LEVEL FLT. WHILE TRYING TO BAL A MINOR FUEL IMBAL OF 200 LBS BTWN THE #3 AND #4 FUEL TANKS; THE #3 FUEL BOOST PUMPS WERE TURNED OFF WHILE THE #3 XFEED VALVE WAS ALSO CLOSED. DURING THE ACT OF ATTEMPTING TO BAL THE FUEL THE SMALL DISTR OF THE CAPT GETTING UP TO GO TO THE RESTROOM; AND THE SO HAVING TO MOVE HIS SEAT FOR THE CAPT TO GET BY WAS CONTRIBUTING FACTOR. AT THAT MOMENT; THE ENG FLAMED OUT. THE BOOST PUMPS WERE IMMEDIATELY TURNED ON BUT THE ENG JUST KEPT SPOOLING DOWN. WE WERE IN RADAR CONTACT SO WE REQUESTED DSCNT TO FL250. AT FL250 WE RESTARTED THE ENG; HAD A NORMAL RELIGHT AND THE ENG REMAINED NORMAL FOR THE REMAINDER OF THE FLT. TOKYO CTL WAS ADVISED THAT WE WERE OPERATING NORMAL AND NO FURTHER ASSISTANCE WAS REQUIRED. MADE A NORMAL LNDG. THE FLT WAS FROM SFO TO NRT AND THE EVENT OCCURRED 10+ HRS INTO AN 11 HR 20 MIN FLT; WITH A SINGLE CREW. THIS MISTAKE COULD HAVE BEEN MUCH MORE SERIOUS HAD IT HAPPENED CLOSER TO THE MIDPOINT OF THE FLT RATHER THAN NEAR THE END.