If you have a flex schedule and the Rachio goes offline, what will occur is that 24 hours after your Rachio goes offline we will initiate our "backup flex schedule." If you had your flex schedule set to run every day, it will default to every 3 days and run on the predetermined start time that you set for this schedule. If you had specific days based on restrictions, we will continue to run on those allowed days as well as at the predetermined start time.
If you had some sort of blackout or something to that effect where no power was being supplied to the Rachio, it would not be able to run at all.
My guess is that the every 3 day backup schedule may not have been enough to keep up with the loss of moisture to those zones while the device was offline. If you are still worried about this sort of thing while you are away, I would suggest having a fixed interval "vacation schedule", which you could turn on when you leave for extended periods. If the Rachio loses internet connection but has a fixed schedule, it will just run that exact programmed schedule using its onboard memory.