Disclosed is a circuit, such as a clock conditioner, that provides an improved ability to exit from holdover operations, most notably during conditions where the clock signal inputs to a PLL of the clock conditioner are significantly out of phase. The circuit utilizes the PLL to generate output clocks based on a reference clock and a feedback clock. During holdover mode, the PLL is unlocked. When the reference clock becomes available and holdover mode can be exited, a holdover controller issues a reset signal that triggers a synchronization of the phases of the inputs to the PLL. The reset signal causes the feedback divider component that generates the feedback clock input to reset its phase and adjust its divide ratio for at least the first divide cycle after restart so that its next rising edge will be phase-aligned with the reference clock. Once the two inputs of the PLL phase detector are phase-aligned, the PLL is re-enabled and the PLL smoothly resumes normal operation.