Absolutely!
-Use the EmuNAND Tool to backup your old EmuNAND
-Backup the contents of your SD card to your computer in two separate folders, ESPECIALLY the "Nintendo 3DS" folder, which is where your games are installed to.
-Take your new SD card and put the Gateway launcher on it, JUST the Gateway launcher when you format your EmuNAND, it deletes everything but the launcher to reformat the card, as it's putting the EmuNAND in a different partition and partitioning the SD card.
-Create a new EmuNAND with the Gateway Launcher by holding down the L button at the Nintendo DS Profile launch and then select Format EmuNAND at the Gateway Launcher menu.
-Take your new SD card with the newly formatted EmuNAND and put it into your computer.
-Copy back over the backup of the old SD card that you made earlier.
-Since we're dealing with two different partitions, at the same time, you can use the EmuNAND Tool to put your old EmuNAND back on the new SD card.
-Once everything is done copying over, go to your EmuNAND the way you always do and everything should be back, with added space.
I've done this quite a few times now for people and every time it works! I plan on buying a 64GB SD card so I have a 128GB 3DS. Cannot WAIT for that!