If you want to keep the EmuNAND, you'll have to format the "new" card with EmuNAND9/GodMode9 to create an SD card with EmuNAND. Then back your EmuNAND and restore it to new card. Copy all the stuff from old card to new.Alright so I'll use the 256 gb SD card, which means I'll have to convert some saves... if I update to boot9strap on my old 3ds SD card, Will I just be able to move everything from that old card to my new one? Even if the old card has the gateway emunand on it still? Thanks for the help and suggestions!
If you don't want the EmuNAND (No Gatewait), then you can just format the new card FAT32 using EmuNAND9/GodMode9/PC, restore EmuNAND backup to SysNAND and copy over the files from old SD card.