The two sensors are a few miles apart
This makes the ChronoDot very well suited for time critical applications that cannot be regularly synchronized to an external clock.
My experiments will be done within half an hour. So, I have to check how much it drifts within that time.
You can use the PPS pin of GPS to get within nanoseconds absolute accuracy. Older GPS to within milliseconds. If the temperature is the same at both units, an Arduino Uno can be calibrated in software to drift 1 PPM. No extra hardware is needed. I did this with PPS pin of GPS, but then you don't need GPS anymore.
if so how would you get a sub-mS deterministic sync through an operating system).