I gather from reports here that the low Li battery warning is supposed to self clear at midnight after a replacement battery is installed. Mine didn't after I'd replaced a 11 month old battery reading about 3.03 V as part of a heater installation and annual maintenance cleaning. I knew that this battery had a full voltage because I tested before I installed it.
Not wanting to wait another midnight to see if the low battery message cleared up, I tried doing a transmitter reset from WeatherLink. I knew this would reset the Console Diagnostics stats and it also apparently works to re-acquire the latest Li battery status because it fixed my battery reading.
So if you have WL and a low battery reading that you believe might be bogus, simply hit the OK button in the Set Transceiver window (without making any other changes there) to force your console or Envoy to update to the latest Li battery status reading.