A disk drive is disclosed comprising a head actuated over a disk comprising a plurality of servo tracks defined by full sectors and intervening short servo sectors, where each full servo sector comprises a preamble, a sync mark, and servo bursts, and each short servo sector comprises a reference pattern and servo bursts. A first phase error is generated based on the sync mark in a first full servo sector, and a disk locked clock is adjusted in response to the first phase error. A second phase error is generated based on the reference pattern in a first short servo sector, and the second phase error is processed to determine whether the disk locked clock slipped a cycle before the head reaching the first short servo sector.