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If you disconnect one of them (the right one when looking from the trunk to the front in my 35d), it will reset your steering and create a DSC warning when starting to drive. You will need to recalibrate the steering. I didn't find this option in Bimmercode and had to go to ISTA-D on a laptop which you can find online. (If you are under warranty, you can still drive it to the dealer and have them recalibrate it for you; just tell them that your batteries drained dead because you had a light on.)
There is no specific coding for the batteries unless you are also going to change them at the same time. The coding applies to the left one and only resets the counters (i.e. date of battery swap and number of hours under-voltage) to allow the computer to make decisions around the life and charging cycles. You can do this through the Bimmercode app. (When I asked them about the 2nd one, they didn't know about it but i realized that it was not being managed by the computer since it doesn't power important items.)
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