I'm not surprised about the angle-of-attack needing correction. The angle-of-attack is defined as the angle between the average chord (an imaginary line running from the leading edge of the wing to the trailing edge of the wing) and the relative wind. Since changing the flap position changes the position of the trailing edge, the angle-of-attack will also change.
Usually you draw a line from the trailing edge (which is sharp so unambiguous) to the point on the leading edge that makes the line the longest.
The definition that makes the most sense, though, is to disregard the geometry of the wing and define zero angle of attack as the zero-lift angle, because then lift is proportional to AoA.
I'm not surprised about the angle-of-attack needing correction. The angle-of-attack is defined as the angle between the average chord (an imaginary line running from the leading edge of the wing to the trailing edge of the wing) and the relative wind. Since changing the flap position changes the position of the trailing edge, the angle-of-attack will also change.