That is the nub...
It is either a "backup Battery" or it is in use in normal flight. If in use, and recharging takes even a few minutes, it is not legal per the regulations.
It can be designed to be, but that opens up the squishy part of "BackUp".
In scuba, if you routinely dip into your back up air, you will get caught out. Likewise in fueling , if you get to using up reserves, you have no reserves.
It strikes me that utilizing a back up battery for mundane power defeats the concept, hence the "Emergency Select" switch I assume is on board.
As with the United Airlines emergency diversion to New Orleans, a loss of a generator caused a distribution problem, blank areas of the panel, etc. What was the state of charge of the two emergency batteries?
Likewise ANA. Did they Take off while charging?
Was the Battery at full charge? Both of them? Did APUBATT start the APU?
Keeping a regulated level of charge (FULL?) throughout the flight means the system is incorporating a safety system into normal flight.
I think the investigation will go in this direction. Lithium actually does look promising as a back up system, but in day to day, not so much.
Service life, maintenance and charging seem to be a weakness in