Flashing firmware image update is easy today, you just need to first stop the Zigbee application using it or temporarly move the dongle to different computer, there are different tools for flashing, see → ITead's "Sonoff Zigbee 3.0 USB Dongle Plus" (model "ZBDongle-P") based on Texas Instruments CC2652P +20dBm radio SoC/MCU
Then it sounds like both you guys also have problem with EMF interference and/or not enough Zigbee Router devices, so make sure read and follow this → Zigbee networks: how to guide for avoiding interference and optimize for getting better range + coverage
Battery drainage is a common symtom of EMF interference and not having enough Zigbee Router devices.