Of course, I actually did it today since I switched from 8GB to 32GBs.
Here's what you'll need to do:
. Copy all the contents from your 4GB SD to PC.
. Make a backup with emunand tool of the emuNAND present in 4GB SD and copy it to PC.
. Grab the 64GB SD and insert it in the 3DS.
. Do not have the Gateway card on your 3DS, you don't need it.
. Run the format emuNAND option in Gateway so you will create emuNAND on 64GB SD.
. Hold power button for a long time until it's completely shut down. Seriously, do it. Do not go to HOME screen.
. Take out the 64GB SD, plug it back in PC.
. Inject the emuNAND you backed up earlier and copy all the contents you had before on 4GB SD to the new 64GB SD.
. Enjoy!
Done, follow the steps clearly and there'll be no problem at all.

You actually do need the emunand tool. I can explain why but I won't bother for now, just do it that way and it'll work fine without a single problem.
