I get to join the club of people with dead batteries. 
I was in a different place for a few weeks. Before I left I checked the voltage of the batteries and had the battery monitor show ~80% charge. Since I have the firmware updates installed and kept the device without charging for longer periods before (periodically checking charge), I felt safe leaving without disconnecting the battery cables.
That was a mistake. When i came back close to a month later, multiple batteries showed low voltages and one of them refuses to keep a charge now.
I couldn’t find the 1800mAh JGNE in stock anywhere. Mixing different batteries is not recommended, so I’ll have to buy a full new set. I can probably find some use for the 7 working JGNEs, but it’s still a waste which should be avoidable.
I looked at the schematic to see how difficult adding an external switch would be.
If I read things right, then disconnecting the fuse F2 will stop supplying the system with power. It should be possible to desolder F2, and replace it with the fuse + an externally accessible switch to cut power externally.
My understanding is that the BGATE pin of the LTC4020 controls the connection of the battery to the rest to the system. Unfortunately, the pin would need to be pulled high to disconnect the battery, so I can’t see any way for software to force a battery disconnect if any cell reaches the lower cutoff voltage.
There’s probably a way to change the circuit to create a software controllable “resettable fuse” (N-channel mosfet in series to the actual fuse?) which could be tripped when a low voltage threshold is reached and reset when the power supply is connected, but doing so would require the LPC to be powered or at least periodically woken up to check the cell voltages and trigger the fuse.
While I confess to not knowing anything about the LPC, this actually sounds feasible as an aftermarket modification. There seem to be unused pins on the LPC, so one of them could be used to trigger the battery cutoff.
I imagine the following steps would work:
- Desolder fuse f2.
- Create circuit with the property of a resettable fuse (mosfet which can be turned off via MCU pin?) and connect this circuit in series with f2 to the original pins for f2. Connect trigger for resettable fuse to LPC pin.
- Change LPC firmware to periodically check cell voltages (potentially waking up from sleep to do so). If any cell reaches a dangerous voltage, change pin value to trigger battery disconnect.
- Connect power supply to restart system and thus reset fuse.
A disadvantage would be slightly increased power consumption / added resistance due to the the new mosfet. Depending on the implementation, turning on the system would require external power (or maybe a push switch to bypass the mosfet?) after the battery pack was disconnected.
Could someone with an actual EE background check the feasibility of what I’m trying to describe here? Such a thing probably already exists; not having read details, e.g. AP91352 with undervoltage lockout sounds related.