Before you transfer your 3DS to 3DS XL, you should back up your SD card. Why, you ask? Here's what happened to reader Kolma.
I didn't and i have paid the price. While everything transferred, licenses, streetpass, everything...All my eShop content is gone and now must be redownloaded. It also means all my eshop save files are gone.
If you're looking for some helpful hints on the transfer process as pertaining to SD card data, check out this feature.