Hi
Yes - stop the timer when the cool down cycle starts.
The logic is that cool-downs are always the same - as fast as possible. So, as far as Roastmaster is concerned, the roast officially "stops" when the cool down cycle begins on roasters like the Genie Cafe, or when the beans are dumped into the cooling tray for roasters with external cooling.
The app will still let you record crack times for a short period after hitting stop, so they can extend past the official "duration" you see in the graphs, but the app doesn't consider cool-down as part of the roast.
Hope this helps - any other questions, just let me know.
Danny