Here's the datasheet for the microcontroller:
http://ww1.microchip.com/downloads/en/devicedoc/39597b.pdfPin 3 can serve either as a TTL I/O port, or as an analog/digital converter. That still leaves it somewhat ambiguous what is triggering the low voltage cutoff.
More information is needed:
1. Follow the trace from pin 3 to see what other components are feeding the signal to it.
2. Put a voltmeter on it in operation as the battery voltage drops below 31.5V.
If the voltage on that trace goes from ~5V to ~0V, this would indicate a TTL I/O port, so a separate component is providing the voltage sensing logic.
If the voltage on that trace goes from ~0V to ~5V, it would also indicate a TTL I/O port, but the controller is looking for a positive "bad voltage" signal. In that case, cutting the trace might disable the low voltage cutoff.
If the voltage on the line doesn't show a sharp transition, it would indicate the pin is being used as an A/D converter. The A/D inputs can use either supply voltage or voltage on pin 5 as a reference. Pin 5 is noted by pdonahue as being the throttle input, so if it is being used as an A/D converter it must be comparing the voltage on pin 3 to VDD. In a way that's too bad, if it had been using pin 5 as the voltage reference we could just play with the voltage provided to pin 5 (a diode on the line to drop the voltage?) in order to make the controller think the voltage on pin 3 was a bit higher.