I updated to the new firmware, no problems! 2 remotes cotrollers, and 3 batteries without any problem, went for the test flight, it works.
The battery update is done in the Pilot App. Once you finished with the aircraft and remote controllers update, you can start the aircraft like normal for the flight. If the battery that is in the aircraft is different then the battery during the update, it will show you the question to upgrade the firmware. You can press yes, the percentage of the update will be shown on the screen, and after is finished will restart automatically and is ready to fly! Remember to keep the firmware .bin file on the SD card for all of the extra batteries!