Before you start, you may want to backup your SD card contents... like the 3DS folder just in case something goes wrong. You can also backup your EmuNAND using this tool here:
http://gbatemp.net/threads/emunand-tool-v1-0.359239/
1. You need to backup the image of the card you are replacing.
2. Write that image onto the larger SD card.
3. Download a free partition managing program (I use EaseUS partition manager)
4. With the larger SD card in the computer, load up the partition program. It will show all your drives and their current file structure. You should see your SD card on there as whatever drive letter it is assignedas . This is what it should look like... I don't have screenshots so I will improvise NOTE: My letters are for labeling purposes:
|__A___=======B=======______________C____________|
A. Is labeled as unallocated space
BUT this is your emunand!
DO NOT UNDER ANY CIRCUMSTANCES MESS WITH THIS!
B. Should be labeled as FAT32 and this is the usable area of the card... like where your 3DS folder and launcher file are, etc.
C. Is the unallocated space that is the extra storage on your larger card.
5. What you need to do is right click the B area and do resize partition. It should bring up a slider or something similiar. You want to to resize it past the space AFTER The partition NOT before!
6. When you are done, it should look like this:
|__A___====================B====================|
There should be no unallocated space after the FAT32. Then click the Apply button and it should perform the action and you are done.