23.9 Synchronization
Both the RTC and the PIT are asynchronous, operating from a different clock source (CLK_RTC) independently of the peripheral clock (CLK_PER). For Control and Count register updates, it will take some RTC and/or peripheral clock cycles before an updated register value is available in a register or until a configuration change affects the RTC or PIT, respectively. This synchronization time is described for each register in the Register Description section.
For some RTC registers, a Synchronization Busy flag is available (CMPBUSY, PERBUSY, CNTBUSY, CTRLABUSY) in the Status (RTC.STATUS) register.
For the RTC.PITCTRLA register, a Synchronization Busy flag is available (CTRLBUSY) in the Periodic Interrupt Timer Status (RTC.PITSTATUS) register.
Check these flags before writing to the mentioned registers.