I've been able to find some good data about the 3DS system transfer, but there seems to be conflicting/incomplete info about the state of the target system.
I have a 3DS (source) and a 3DS XL (target). On the 3DS I have Pokemon X downloaded, on the target XL I have Link Between Worlds. There's also some save data on both, but it's not a huge deal if I lose it. Both are linked to the same Nintendo account.
Will I permanently lose my games on the target, or will I retain them? (It's fine if I have to redownload Zelda). What will be the exact state of the target? From what I understand, I'll have everything on the source's SD card, and the target's is invalidated (except for pictures and sound), but that doesn't tell me much about the licenses I still own on the target.
Best Answer
A 3DS system transfer will, as you have mentioned, keep the source SD card as it is, and replace all software and save data of the target.
In addition, eShop accounts will be merged. This means that your digital copy of The Legend of Zelda: A Link Between Worlds will disappear from the target system, but will be ready for re-download, together with all eShop titles you previously purchased. Money in the two eShop accounts will merge, too, and be added to each other. You will, however, have to remove any linked Nintendo Network IDs from the target system.
Source and more information here.