When you plug the battery in the charger you hit the calibrate/performance button (it's in between the two charging sleds.) Instead of green progress bars you'll get a red light. The charger does a full dump & charge to recalibrate the battery. *Takes about 10 hours.
It's standard on all of the 1D series cameras.
*It won't force you to do it if you don't have the time for the recalibration.