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Речь идет о Prescaler? тогда поищите в даташите комбинацию "Prescaler Reset".
Для ATMega128 в регистре SFIOR есть бит PSR321: Prescaler Reset Timer/Counter3, Timer/Counter2, and Timer/Counter1
описание:
When this bit is one, the Timer/Counter3, Timer/Counter1, and Timer/Counter2 prescaler will be reset. This bit is normally cleared immediately by hardware, except if the TSM bit is set. Note that Timer/Counter3, Timer/Counter1, and Timer/Counter2 share the same prescaler and a reset of this prescaler will affect all three timers.