WHen you register a battery in a modern BMW, there are two things:
- the type and size
- the age counter that needs to get reset when you add a new one
So, if you are just disconnecting the old battery for maintenance, when you reinstall it, there's no need to change any of those programmable items. But, when you install a new one, or the type or capacity changes, it will not get charged properly and its life will be shortened as a result. The computer adjusts the charging regime based on those parameters, so it would think it had an old battery in there, and adjust itself accordingly.
If you have a BMW battery, all of that can be done by entering the battery serial number, if I remember correctly. The BMW computer seems to just read the bar code, so it's easy for the tech.