I just double checked my moisture level charts from last Tuesday when I had to do some manual watering, and all the watering I did is reflected in the charts, and taken into account for the calculations of when the system next needs to water. I'm also running Flex. I love that the Rachio does this!!!
Whether the zones will water the next day or not will be dependent on how much moisture the plants are predicted to lose the next day, and precipitation forecast, etc., but the watering will not just be wasted like it was on the Rainbird.