Yes, it's one of 3 choices given in the middle of the transfer.
- Wireless Transfer: The 3DS copies all of the files to the other system's [micro]SD card for you. This is really, really slow.
- Low-Capacity microSD Card Transfer: All of the eShop games are deleted and their saves backed up, and are redownloaded on the new system. Don't pick this especially if you want any chance of keeping Ironfall: Invasion!
- The best option: PC-Based Transfer: Use a PC to copy all of the contents to the new [micro]SD card. If all of the content is already on a microSD card, just insert it in the new system!