I'm guessing the controller reports 0 volts, 0 amps, and -1%, which I recall is what mine did when I had the SMBUS disconnected. Does it not give you the "Solo battery is too low for flight" message, or flash low battery in those conditions? I would it recognizes the lack of battery data as just that, rather than taking it for zeroes and reporting it as too low. Disabled the battery failsafes? Operationally, just going by a traditional timer based on standard performance, and taking cues from the LiPo alarms if it gets mad?
Also I presume this defeats the pixhawk's ability to scale the motor output to the voltage? Did you change those parameters to disable it or just leave it?