20.5.3 Using the Output Compare Unit
Since writing TCNT01 in any mode of operation will block all compare matches for one timer clock cycle, there are risks involved when changing TCNT0 when using the Output Compare Unit, independently of whether the Timer/Counter is running or not. If the value written to TCNT0 equals the OCR0x value, the compare match will be missed, resulting in incorrect waveform generation. Similarly, do not write the TCNT0 value equal to BOTTOM when the counter is down counting.
The setup of the OC0x should be performed before setting the Data Direction Register for the port pin to output. The easiest way of setting the OC0x value is to use the Force Output Compare (FOC0x) strobe bits in Normal mode. The OC0x Registers keep their values even when changing between Waveform Generation modes.
Be aware that the TCCR0A.COM0x[1:0] bits are not double buffered together with the compare value. Changing the TCCR0A.COM0x[1:0] bits will take effect immediately.