Yes, your a2c will change by whatever you reduce the travel by. The spring rate will also be affected so you will have to add a few more psi to achieve the correct sag (according to the Fox link below). Keep in mind that reducing the travel will also change the geometry of your bike.
Take a look at the link below. Go to Forks, 32mm, 32 Float 29, and take a peek at the suggested air spring settings for the various travel heights.