Good question... I guess it all depends on how duenna handles it. I assume that the "flight time" will be paused, while the "baton time" keeps ticking. The race time is taken from the "flight time", so if that's the case, then a pause will work just fine.
Good question indeed. I don't know the answer. Guess a quick test is in order. Howerver, in my understanding Duenna references the RW clock, not the FS clock, so flight time would advance as well as baton time even though the flight is paused. So in urgencies you can pause the flight, but the clock will continue to tick on.