Force TCNT to stay below OCRxA on ATmega328P
Can I manually jump to an ISR regardless of its "normal" trigger?


This should be possible, but is probably not the best solution.


  This is certainly an X -&gt; Y problem, so I'm open for other
  approaches.


It would seem you are using the timer in CTC mode. In this mode, when
you write to OCRxA, the register is updated immediately, which leads
to the problem you are experiencing. The solution is to instead set the
timer to “fast PWM” mode. In fast PWM mode, the OCRxA register is
double buffered: you will be actually writing to a buffer register, and
OCRxA is automatically updated from that buffer on the same timer
clock cycle that clears the counter.

It may sound counter-intuitive to use a PWM mode when you do not need
the PWM feature. However, as long as the “compare output mode” is set to
“normal port operation” for both channels, the timer will not generate
any PWM output, and you can legitimately use the fast PWM mode only for
its double buffer feature.