So you are using 2 timers to make 1 pulse?
Well, I can say that interrupt latency can be accounted for by ADDING a reload value to the accumulated timer value.
And nothing in your ISR is using PBP's system variables, so the handler "Type" can be ASM, which will reduce the latency to be accounted for.
I won't go into too much detail because I think you're probably doing it the wrong way.
What are the minimum and maximum pulse widths?
And what is the interval between them?
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