BQ76940: short phenomenon

Hi Fawn,
1. The bq76940 does not have a VCC designation, so I may be misunderstanding the issue. If one of the power supply pin pairs (VBAT in the data sheet) is shorting one might expect a high voltage is being induced during disconnection. Normally it might be expected that the voltage of the capacitors would dissipate slowly after disconnection. You might check to see if some of the device pins still have power while others are pulled down to the lower part potential (or pulled up to the upper part potential). If it is the input pins, disconnection is not expected to be a concern since the input filter capacitor voltages should slowly decay. Connection may be a larger concern, see #2.
2. Cells 1, 6 and 11 have the lowest single ended voltage limit in the device. The phenomena of the different filter capacitor sizes shown in figure 21 of the application note www.ti.com/.../slua749 may be occurring. This could put a high voltage on cell 11 or cell 6 which could stress both the single ended limit or the differential limits of those pins. Cell 1 should not normally experience a high voltage. Note that the reference of the device is recommended to be connected first, this would apply to the upper part as well. If the upper device's cell 1 was connected without the cell connection for its VSS, this could provide a high voltage on the pin much like figure 21.
Battery separation or loss of a battery in the stack or broken weld in the cell assembly can result in a large differential positive or negative voltage on the related cell inputs. This can be damaging since even with the input filter resistors the currents may be large with the large voltage. Some designers will provide zener diodes at the cell connection, these can carry some transient currents but typically can't support the full system current if the battery separates under load.
The zeners at the cells can help with cell connection by distributing the voltage at the connector, but will not completely protect the device since the filter capacitors hold the voltage at the IC pins with large momentary voltage drops across the filter resistors. Limits on the cell input voltages may be needed such as the D11 and D10b in figure 21. Each system may need to be inspected for the type transient which occurs in that system and a specific protection method designed.