"Percentage" stems from comparing like qualities. If we start with a circle of radius r and end with a circle of radius R, then the change in area of this circle would be pi*R^2 - pi*r^2, or pi(R^2-r^2).
The ratio of this change to the original area, which was pi*R^2, would then be
pi(R^2-r^2) R^2-r^2
-------------------- = ------------
piR^2 R^2
If you want the percentage change, then multiply the above result by 100%.