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.