One notable fact is that extending the flaps using alternate power is a irreversible thing inflight. You will not be able to retract them again in the air.
In what aircraft?
In aircraft I've flown with an alternate means of operating leading edge and trailing edge flaps or devices, (the question and the replies thus far don't state which), the device can be extended and retracted under alternate power.
As Dream747...the flaps when operated under alternate power (electric motors) in the 747...can be extended and retracted in flight, and on the ground. Same for the leading edge devices. I the case of the leading edge devices, arming the system permits continued operation using pneumatic crossbody bleed air, and when the alternate leading edge switches are used, the bleed is bypassed for the use of electrical power. In the case of the trailing edge flaps, arming the alternate switches disables the hydraulics by putting them into bypass, until the arm switches are shut off. When the arm switches are shut off, the hydraulic operation of the flaps resumes. If the hydraulics for the trailing edge are left in bypass, the flaps may be raised and lowered using the electric motors controlled through the alternate trailing edge flap switches.
This brings up the obvious...when one asks a question such as "why is the switch red?" this leads one to wonder which aircraft it is to which the speaker is referring. Of hundreds of airplanes and tens of thousands of switches an switch combinations, one might be a little more specific.