nope, they should be stored there, or you can re-download from the eshop i believe as long as you have it connected to the NNID and such.
so basically, take the regular sd card from your current console, put it in, drag it to desktop or save it. then when you get a new console, insert the micro sd if you can, drag your data over to that and should work.
you might want to ask the staff there since i did this between the regular 3ds and a 3ds xl not the newest ones