you use luma cfw yes? do you have a9lh installed ? or are you an menuhax user?
if you are on a9lh that would be very easy for you, you could simply backup your current emuNAND that you have on your 16gig card and then back it up on your pc, then power off your 3ds push your new 64gig card in and boot your 3ds into D9 and then simply restore your emuNAND with the option stating (restore emuNAND a9lh) something like that, then after that i belive it formats your sd card and you will have your emuNAND back on the new card.
after that simply eject your new SD card and copy all of the content that was in your 16gig card into your 64gig and push your 64gig back in your 3ds and it should show up your emuNAND with your content.