I've heard of keeping the updated firmware.bin file on your microSD when you use a new battery is a thing. Do batteries have to be updated? What if I buy a battery and forget to put the *.bin file on the microSD card? Would it just not work?

Right -- you should always keep the latest firmware on your memory card. That will allow the DJI Pilot application to install the firmware on your batteries as needed. You don't need the latest firmware updates to fly your Phantom. However, it's best to use the latest version -- as it should be the most bug-free.

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PhantomHelp.com Posted at 2015-6-16 10:08
Right -- you should always keep the latest firmware on your memory card. That will allow the DJI Pil ...

Yeah, Right, that's why since I updated to FW 1.1.9 and now 1.2.6 I can't even fly the thing!!!

If you have flown with al your batteries you can delete it them right?

Point 1 - not every firmware update includes a battery firmware update. If a battery firmware update is included in the .bin file, the battery firmware will be updated at the same time as the Phantom aircraft firmware is updated.
Point 2 - In some cases, if you put a new battery in the Phantom and it is missing the latest firmware update, the Phantom may not operate and you may not be able to link to the RC.
Point 3 - YES - after you have updated the firmware in all your batteries, you can delete the .bin file from your SD card.  If you buy a new battery at a later date, you should always put the latest firmware .bin file on the SD card and put it in the Phantom before starting up that battery the first time, in case it needs a firmware update.
Point 4 - Remember, when updating the Phantom aircraft firmware and/or the Phantom battery firmware, leave the Remote Control OFF and then turn on the aircraft battery.  If after the gimbal dance finishes you hear only a single D-DD beep from the Phantom, no firmware update was required.  However, if it starts a series of D-D-D-D beeps, then a firmware update is in progress.  Wait until the beep pattern changes to D-DD, which means the update is finished and you can power off the Phantom battery.  Battery firmware updates typically only take a couple minutes each.

Hi guys, there is 5 threads on battery firmware, yet no real answer for what to do if you buy a new battery and already have update the aircraft to the latest firmware 1.4.001. There seems to be consensus that batteries need to have v1.3.20 installed, but we don’t know what they come with, so how do you be sure to have v1.3.20 onto the batteries if you have 1.4.001 on the bird. Downgrade the aircraft and load batteries, then upgrade again?
http://forum.dji.com/thread-18636-1-1.html, http://forum.dji.com/thread-31335-1-1.html, http://forum.dji.com/thread-22201-1-1.html, http://forum.dji.com/thread-21437-1-1.html, http://forum.dji.com/thread-18636-1-1.html. Might be useful to consolidate the threads and try to get a consistent set of advice.

david.p.mann@ea Posted at 2015-6-17 00:21
Point 1 - not every firmware update includes a battery firmware update. If a battery firmware update ...

Additionally, during the battery update, the two center leds on the battery will flash as the update is performed...

GeeDee Posted at 2015-10-2 10:45
Hi guys, there is 5 threads on battery firmware, yet no real answer for what to do if you buy a new  ...

If the battery firmware needs to be updated it will happen automatically if you turn on the Phantom 3 with the firmware .bin file on the micro SD card in the camera SD card slot.  It doesn't matter if the Phantom 3 firmware has already been updated. This is exactly the case if you need to update firmware on multiple batteries. After the first update cycle when BOTH the Phantom 3 aircraft AND the battery firmware are updated, you turn off the Phantom 3, put the next battery in the aircraft, and turn it on again. This time only the battery firmware is updated. Battery firmware updates are fast - typically take less than two minutes.  Same beeping sequence applies - D-D-D-D (during update) changing to D-DD when finished.