What is the battery voltage supposed to be in flight?

As Albert Says; There is nothing wrong with your battery.

If the battery was truly Not being charged, after about three flights, the engine would no longer start.
The Lane Voltage data comes from the CAN-BUS.
The Battery voltage displayed is likely the Voltage seen by your EMS, Not the actual battery voltage.
There will be some voltage drop in the wiring harness from the battery to the panel.

As a temporary test, Activate your EMERGENCY BACKUP POWER SWITCH.
This will connect the ECU BUS, Lane A, Lane B, and the Battery all in parallel.
All the voltages should be the same.
If the Battery is still displaying LOW, you have a display issue.

It is not uncommon for EMS displays to have settable calibration factors to compensate for harness losses.

Albert Yowell wrote:

Any 12V lead-acid battery from your Cub Cadet to you Caterpillar 930 wheel loader has 2.1v per cell. 2.1x6=12.6. So a 12.6V means the battery is healthy, but not being charged. 

Thanks, Albert! You are right! Got this sorted yesterday. Healthy battery. Healthy stator, too. Some electrical connector was burnt out. Not exactly sure what it was, but my avionics wizard was able to fix it in about an hour or two and now I see 13.6 volts on the battery when flying!