Since writing TCNT2 in any mode of operation will block all compare matches for one timer clock cycle, there are risks involved when changing TCNT2 when using the output compare channel, independently of whether the Timer/Counter is running or not. If the value written to TCNT2 equals the OCR2x value, the compare match will be missed, resulting in incorrect waveform generation. Similarly, do not write the TCNT2 value equal to BOTTOM when the counter is counting down.
The setup of the OC2x should be performed before setting the data direction register for the port pin to output. The easiest way of setting the OC2x value is to use the Force Output Compare (FOC2x) strobe bit in Normal mode. The OC2x register keeps its value even when changing between Waveform Generation modes.
Be aware that the COM2x[1:0] bits are not double buffered together with the compare value. Changing the COM2x[1:0] bits will take effect immediately.