Disk drive employing fly height calibration tracks to account for magnetic entropy and thermal decay

A disk drive is disclosed comprising a head actuated over a disk comprising a plurality of tracks including a first fly height calibration track and a second fly height calibration track. The disk drive further comprises a fly height actuator operable to control a fly height of the head in response to a fly height control signal. When a refresh event is detected, calibration data is written to the second fly height calibration track. After writing calibration data to the second fly height calibration track, the first fly height calibration track is read in order to calibrate the fly height control signal applied to the fly height actuator. After calibrating the fly height control signal, the second fly height calibration track is read in order to recalibrate the fly height control signal applied to the fly height actuator.