Boron Not Charging

I have a Boron deployed to a site where it monitors solar power for another system. The Boron is plugged into a 5VUSB power adapter which is fed from a large lead acid battery. Occasionally the lead acid battery is disconnected if enough solar is not available. The Boron's 6000mah battery then takes over. The issue I am having is that the charge state is always "Not charging" and power source is VIN. Essentially the lipo is never recharged. Once on site I noticed the charge LED will not turn on either. Tried another lipo, another usb cable and double checked other devices charge from the USB port.

The only power management code in my firmware is to prevent charging below 32F:

void enableCharging()
 {
       auto powerConfig = System.getPowerConfiguration();
    if (powerConfig.isFeatureSet(SystemPowerFeature::DISABLE_CHARGING)) {
        powerConfig.clearFeature(SystemPowerFeature::DISABLE_CHARGING);
        System.setPowerConfiguration(powerConfig);
        chargeOn = true;
    }

   
 }
void disableCharging()
{
     auto powerConfig = System.getPowerConfiguration();
    if (!powerConfig.isFeatureSet(SystemPowerFeature::DISABLE_CHARGING)) {
        powerConfig.feature(SystemPowerFeature::DISABLE_CHARGING);
        System.setPowerConfiguration(powerConfig);
         chargeOn = false;
    }
}

Somehow in the process of trying different batteries etc. the SOC went from 30 to 75%. Trying to understand if this is a hardware issue with the PMIC or a charge voltage calibration or something else. Will go back to site and measure some voltages with the meter.

Update on this. At the site I unplugged and plugged in the charger a few times. Switched to stock Blink firmware. Then tried another USB power supply with no peripherals (no sensors, just the Boron). At some point it never came back on and the board was warm. I assume this was some sort of hardware issue with the PMIC chip.
I am trying to understand what might have caused the hardware issue. Has anyone had issues with transient voltages damaging the Boron or charge controller?

It does sound like the PMIC (bq24195) was damaged. The maximum on VIN is 17 VDC; on the Boron this is the VUSB pin. It's not protected against transients within the chip; it's expected that you will do that in your circuitry. For example, when powering from a vehicle see the vehicle power design note.