Rachio 3 not registering usage, soil moisture

I am entering my 3rd season with the Rachio 3 controller and everything has worked fine in the past. This year when ‘enabling’ the controller I noticed that the Rachio Wireless flow meter was offline (batteries were dead). I replaced them but was still unable to pair with the controller (which as not totally unexpected as the flow meter is far away from the controller and has always had a weak signal). Anyway I simply removed the flow meter for the time being. The system is set to use smart watering with 4 different zones configured. It has run as expected the last 2 nights for the proper zones but this morning I noticed that the usage has been recorded as 0 minutes and the zones have a reported soil moisture as 0% even though the system did run. History has been recorded as the system running for the correct times and of course I can see the ground is wet. With the usage and soil moisture incorrect it wants to run again and again which is clearly wrong.

Please help. Thank you.