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I know, flaps are mostly used during take-off or landing to generate both lift and drag simultaneously.
I am wondering if the pilot uses flaps to generate more lift so that they can climb in less distance (due to drag of flap) and possible reasons for doing it. I have an idea that the flight control system may prohibit flap deployment above a certain altitude or at higher speeds due to flap structural limitations.
It's a little complex, but here is a shot. Take a look at the following graph:
graph http://www.navlog.net/wp-content/uploads/2012/10/PowerAvailable.png
What you can see is multiple airspeeds. For a plane, the rate of cruise is maximised around Airspeed B is reached- this is when the difference between power available and power required is the greatest and therefore the most excess energy is available for climb.
The slope here indicates how much power is necessary for that airspeed- the steeper the curve, the worse it is. The value is really high for airspeeds all the way to left.
If you were to deploy the flaps, you would sort-of shift the power required curve to left- adding drag, reducing the difference between the power available and power required, reducing the maximum rate and in the process increasing the power necessary.
(source: ppl-flight-training.com)
In the equation above, you want to increase lift. Yes, you can do this with flaps- it would increase CL. As you yourself state, it takes a lot of drag to use flaps and slats. Another option is to increase velocity. This is more efficient and uses less energy.
The reason we need is flaps is since as the velocity drops for landing, we need to increase the CL to maintain sufficient lift for landing. Airspeed for B for landing though is much too fast, so you want to slow down to the left side of the graph. See this post on a little more detail on this relationship.
As for flap limitations, they appear to be 20,000 ft for the Boeing 737- Mostly because boeing found them unnecessary to use at higher altitude.
Most planes have a flap extension (Vfe) speed limit. Deploying them at cruise speeds will damage something. Even small planes have a limit, example for a 172:
VFE Maximum Flap Extended Speed: KCAS KIAS Do not exceed this 10° Flaps 107 110 speed with flaps 10° to 30° Flaps 85 85 down.
One may have trouble getting the plane to go that fast with the flaps down, but once they are retracted and speed increases, deploying the flaps above those speeds may damage something.
