This is taken from a Boeing Airliner magazine:
Several operators have asked Boeing why the Airplane Flight Manual has a limitation restricting the use of flaps above 20,000 feet. The reason for the limitation is simple; Boeing does not demonstrate or test (and therefore does not certify) airplanes for operations with flaps extended above 20,000 feet.
There is no Boeing procedure that requires the use of flaps above 20,000 feet. Since flaps are intended to be used during the takeoff and approach/land phases of flight, and since Boeing is not aware of any airports where operation would require the use of flaps above 20,000 feet, there is no need to certify the airplane in this configuration
Sometimes it pays to save old responses
Mutt.