It is possible to change the update period of synchronous channels while they are enabled. See Method 2: Manual write of duty-cycle values and automatic trigger of the update and Method 3: Automatic write of duty-cycle values and automatic trigger of the update.
To prevent an unexpected update of the synchronous channels registers, the user must use the PWM Sync Channels Update Period Update Register (PWM_SCUPUPD) to change the update period of synchronous channels while they are still enabled. This register holds the new value until the end of the update period of synchronous channels (when UPRCNT is equal to UPR in PWM_SCUP) and the end of the current PWM period, then updates the value for the next period.