Again you are assuming this action is carried out at a safe height. What would happen, for example, if a pilot were to retract full flap at say, 100ft on the approach when the airspeed has decreased to such an extent due to the resultant drag?
It's true that if the aircraft were at or below the zero flap stalling speed, raising the flaps would require an increase in AOA that would produce a stall.
However, if the pilot has slowed to such speeds, it's because he has the mistaken (but intuitive) belief that the elevator is the "up" control. Sometimes it is, sometimes it isn't.
The flaps alone will not slow him to this speed, because the the drag alone produces a greater descent angle, not an airspeed reduction. The airspeed reduction, as always, is proceduced by an AOA change. However, sometimes flaps produce a pitching moment around the CG which, in effect, retrims the airplane for a different airspeed. In the Mooney I fly, flap extension will *increase* the airspeed, not reduce it.
Regardless, most pilots realize well before 100 ft that they won't make their target. If they're on airspeed, as they should be, raising the flaps won't cause a problem.