Stoney74: Your asking fairly complex question, i'll out line for you most of the forces at work.
Lift:
When lowering flaps assuming no aoa change do to other forces lift will increases as flaps start to be lowered.
This lift has 2 effects, If the Center of pressure of the lift does not move the extra lift will create a pitching down force do to th cl /cg relationship. But do to the increased lift the plane will also start moving up,and do to that upward movement the AOA on the tail will change causing a pitch up force.
Drag:
Drag will typically increase as you start to lower flaps. If you have a Hi wing plane this extra drag will produce a pitch up torque. On a low wing plane it will produce a pitch down torque.
Center of lift i.e. pressure.
Depending on the flap type the the CP will move. If it moves back, it will create a pitch down torque, if it moves forward a pitch up torque.
Lift moment. As airflows over and under a wing, more drag is created on one side of the wing than the other. This different in drag of top vs bottom of the wing creates a pitching torque. How much torque and direction can change with different flap types.
These are the basic forces at work, sum up all the torques , what ever direction the sum is, determine what direction the plane will rotate.
HiTech