You can do that in a pinch...we have done it on several jobs where what the customer wanted was not available in a replacement offering. The drawback to it is usually the frame is thicker so you loose more visible glass than you would with a true replacement, and a replacement is designed to fit into the frame of another window and be screwed in place, and the screw holes are pre drilled where that will not do any damage to the hardware of the window, drilling yourself you may hit a locking mechanism or other piece of hardware that would have to be replaced. You should be able to order the new construction window without nailing flanges as in many applications nailing flanges can not be used (ie concrete walls in some ICF houses)