I wouldn't remove it - you're going in for a battery after all.
Now, if you were throwing codes, then yes, remove it. I left my intake in (More and then FFV) an several service calls and never had an issue with warranty work. Then when the temp sensor wire had a short (by then the stock intake was back in place just by chance) they repaired it under warranty, even though there is a chance that pulling the airbox out created the short in the wiring
Just leave it in place, and let us know how the dealer treats you on the battery.