I won't tell you it's right or wrong, but suggest keeping a battery or two separate. One for each drone, not mix and max. Unless you wish to update all of your intelligent flight batteries, and they should both still be good/safe to use in either of your Phantom 3 drones.
If your drones are both trouble free, as my awesome Phantom 3 Pro has been/is, updating shouldn't be an issue for you. But if you are happy, flying on any of the previous versions, that's up to you. Enjoy!!
Some updates May and very well, eventually Will be mandatory. You might get 5-6 flights before the drone won't fly without the fresh firmware or app.
I prefer to just stay current, and enjoy the luxury of not having to be concerned about which of my 4 intelligent flight battery is usable or not. ;-) just charge and go.
Imagine someone with two or three different models of previous Phantoms, and now their need for three different sets of batteries.
You're lucky, both drones can fly on the very same packs.
Just update, and be done with it. Or buy more!! Hahaha
RedHotPoker