Its actually common (Id say normal) when dealing at aircraft level to ignore the local chord line and simply define AOA by reference to aircraft level geometry.
Angle of attack for the aircraft then becomes the angle between the aircraft reference line and the free stream (far field) air flow, much as pitch attitude is the angle between the same aircraft reference and the ground plane.
Only when this is done can the 'normal' relation ship between angle of attack alpha, pitch attitude theta and climb angle (flight path angle) gamma hold in still air:
theta=alpha + gamma
if you start accounting for wing geometry changes and the like it's extremely difficult to simply model aircraft dynamic for changing configurations. it also becomes a mess trying to analyse aircraft aerodynamic data consistently, or to correlate things like AOA vanes on the fuselage with aircraft behaviour.
the 'chord line' concept is fine when comparing aerofoils, but it's just an impediment when dealing with a real aircraft - what about washout? what about aeroelasticity? and so on.
so to answer hawk37, if the gamma does not change due to the slat deployment, then neither does alpha.