removing batts for a while (weeks even I'm sure) is fine.
I just recommend you leave the trunk lids opened.
you do not want these closed with no battery as it becomes a little more of a pain in the butt to get into a locked trunk (if you close/latch it).
you could also just put a cloth over the latching mechanism in the trunk as well to stop the top hatch from locking into the bottom.
Do you have a car port or garage to keep the vehicle?

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I swear, my cars are like a girlfriend.
Sometimes its a rough ride, sometimes its smooth motorin'.
Sometimes she doesnt like how i treat her and sometimes i dont like how she behaves.
BUT at the end of the day, she loves it when I am inside her.

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'91 850i
'05 X5 4.4i
'09 Clubman S