Hi
at the moment I have a Phantom 3 Advanced and a Phantom 3 Standard.
Recent firmware updates for them have included updates for the battery.
I am used to swapping the batteries between the two quads.
Is there a problem doing this with the different firmwares for the batteries?

It would be best to have the most current firmware for all batteries.  Why can't you update them all and use them for both devices?
There are also often fixes to past problems, that aren't listed in the firmware liner notes. So having the most recent one is optimal.

But it's up to you, how you choose to utilize your flight kit. I always keep my drone, RC and batteries current, if there are updates.

RedHotPoker

Updates has also been known to break things. So do you feel lucky?

Sometimes it is best to wait until the dust settles and all of the lemmings have tried it first.

Sure, in my experience i'll never do a new update...my p3s has been in the box too long time cause 1.6.8