Alright, let me take a crack at this one. Remember, Angle of Attack is the angle between the relative wind and the chord line of a wing (thinking light, GA aircraft wings here). Chord line is defined as leading edge to trailing edge. When we lower flaps, we have changed our trailing edge position and increased the angle of attack. Therefore we are generating more lift due to a higher angle of attack.
I would say that the wing will stall at the same angle of attack, although our relative pitch attitude will be lower than that of a normal stall.
As a really bad example: Let's say our pitch attitude and chord line were the same. So if we pitched up 10 degrees, so would our chord line and our angle of attack would be also 10 degrees. Let's also say that we find our aircraft stalls at 18 degrees. Let's also say that lowering our flaps increases our chord line by 5 degrees. So at level flight (0 pitch up), our angle of attack is now 5 degrees. Given the wing previously stalled at 18 degrees pitch up, I would say we should stall at 13 degrees pitch up (with flaps, the wing is still at 18 degrees). Thus, with flaps, we stall at a lower pitch attitude but the same angle of attack.
This assumes no power, constant weights, slotted or plain flaps (IE no change in surface area).
So that's my take on it. Could easily be way off the money.