Due to limited memory on these devices, you will need to deactivate the main.py script running on the unit in order to have root to update the firmware.
This can be done from the Device Cloud by selecting the Properties for your unit, followed by Python. Uncheck the main.py entry, under the Auto-start Settings. Reboot the unit by selecting the Administration option for your device (back on the Devices screen), followed by Reboot.
Once the unit reconnects to the Device Cloud run the firmware update. Once the firmware update is complete, re-enable the main.py script to auto-start and reboot the unit again.