When a general register is used, since the cycle value set to the counter does not match with the newly set value, the timer continues to count until it overflows. After that, the counter operates at the changed cycle value.
When a buffer register is used, the timer operates at the changed cycle value after it operates at the current cycle value.
The above mentioned applies to the duty factor.
To change (update) the cycle and duty factor, pay attention to the differences between the general-purpose registers and buffer registers, the values to be changed, and the timing of the change.