A disk drive is disclosed comprising a head actuated over a disk comprising a plurality of servo sectors defining a plurality of servo tracks, wherein the servo tracks form a plurality of servo zones, and a servo data rate of servo sectors in a first servo zone is different than a servo data rate of servo sectors in a second servo zone. A disk locked clock is synchronized to the data rate of the servo sectors in the first servo zone, wherein the disk locked clock for generating a timing window relative to the servo sectors. When the head crosses from the first servo zone to the second servo zone, at least one of the disk locked clock and the timing window is adjusted to compensate for a timing transient.