Since writing TCNTn in any mode of operation will block all compare matches for one timer clock cycle, there are risks involved when changing TCNTn when using the Output Compare Unit, independently of whether the Timer/Counter is running or not. If the value written to TCNTn equals the OCRnx value, the compare match will be missed, resulting in incorrect waveform generation. Similarly, do not write the TCNTn1 value equal to BOTTOM when the counter is down counting.
The setup of the OCnx should be performed before setting the Data Direction Register for the port pin to output. The easiest way of setting the OCnx value is to use the Force Output Compare (FOCnx) strobe bits in Normal mode. The OCnx Registers keep their values even when changing between Waveform Generation modes.
Be aware that the TCCRnA.COMnx[1:0] bits are not double buffered together with the compare value. Changing the TCCRnA.COMnx[1:0] bits will take effect immediately.