Updated software last night

I clicked update last night. This seemed to complete ok then it started the calibration.
Batteries were dumped as expected but now the inverter is idle and it says it can not see any batteries.
Is this normal?

No, check what's in the inverter log, but you should see firmware update, calibration starting, then another for when discharge starts, then a 3rd one for when calibration finishes.

After the firmware has updated there's no further reboots of the inverter so it shouldn't loose sight of the battery

Suggest you check the logs then call givenergy support