An endpoint or other communication device of a communication system includes a clock recovery module. The communication device is operative as a slave device relative to another communication device that is operative as a master device. The clock recovery module comprises a clock recovery loop configured to control a slave clock frequency of the slave device so as to synchronize the slave clock frequency with a master clock frequency of the master device. The clock recovery module further comprises a discontinuity detector configured to detect a delay discontinuity in timing messages received in the slave device from the master device, and a loop controller operative to place the clock recovery loop in a particular state responsive to the detected discontinuity. The particular state comprises a state in which a normal operating mode of the loop is interrupted and a compensating drive signal is applied to a clock source of the slave device to at least partially offset phase error accumulation associated with the detected discontinuity.