Rake relative to the frame would remain constant, but rake relative to the ground would increase slightly by lowering (softening) the rear end of the bike. This would increase the bike's trail which would increase its stability in straight line riding, but decrease its nimble qualities on curves.
You probably understand what 'trail' is but for those who don't, I'll try to explain. Trail is the length of the space on the ground between the fork's projected axis to the ground and a vertical line dropped to the ground from the front axle. As the amont of trail is increased, the bike becomes more stable but less nimble.
As Fulltilt1 suggested, lowering the front corresponding to lowering it in back would preserve the bike's original trail, but I don't feel that I'm competent to be messing around inside the forks.
Anyway, after all the discussion about how softening the rear suspension could effect handling, and given my limited mechanical competence, I returned the bike to its factory setting and immediately noticed an improvement in its handling at the expense of its ride becoming more harsh. Having tried it both ways, I can see some wisdom in the factory setting.