Wing loading is measured in units of weight per unit of wing area, and the airfoil has no direct impact on wing loading. Changing the size of the wing or changing the flying weight will change the loading.

Be aware that some flat bottom airfoils need to fly with negative incidence or engine downthrust. The Clark Y on the J-3 Cub is a classic example of this. If you simply slap the flap bottom wing in place of the semi-, it may surprise you on the first takeoff by leaping skyward. Be prepared to either shim the trailing edge up or add engine downthrust, maybe both. Again, the swap may work perfectly, but there is the possibility that it will need more trimming than you might think.