You're probably using emunand, and need to copy the partition over.
I'm going to assume you only have one SD card reader on your computer, if you happen to have two, you can probably use a free partition manager to make this easier.
Download Win32 Disk Imager. We're going to make an image of your old sd card, and write it to the new sd card.
Put in your original 32 gb sd card, run Win32 Disk Imager, select your device and pick a place to save your image. Then click read.
After that is done, take out your old sd card and put in the new one. Run Win32 Disk Imager, pick your image and device, and then click Write.
After it is done, throw the new SD card in your 3DS, everything should be working. But unfortunately, it will only show up as the size of your original card.
Throw it back in your computer, run either Aomei Partition Manager or EaseUS Partition Master and you can resize your partition to the full size of the card.