If it's just that one plane that has it on the wrong switch, you'll have to edit that plane using the Aircraft Editor. Go to the Radio tab (at the bottom of the screen in the Editor), then drill into Software Radio. For each channel, look at the settings for "Input". You'll have to figure out which RealFlight Channel is on your Switch C, and then change the Input on that channel to point to RealFlight Channel 6 instead.
If the flap switch is wrong on ALL planes for some reason, then you may have accidentally changed something in the Controller Profile.