The only thing I would be worried about is that if they decide to change your system because the repair isn't possible, they will send you back a regular edition 3DS XL instead. This happened to my friend, his old Zelda edition had a loose touchscreen, and when he sent it they called him to say they had to replace the whole system, and ask if he wanted a black or aqua blue replacement, because they don't keep special editions in there.
Otherwise, I really have no complaint, on the contrary. Service is fast, doesn't cost a thing, and is pretty great. But yeah, I would probably call them first to ask if that's a problem that requires changing the whole system, if you want to make sure you keep your special edition