I'm very curious if this is possible. I don't have any games downloaded on to my 3DS but I have a ton of hats and completed puzzle pieces that I want to know if I can transfer. Also, can I copy the 3DS's SD card to my computer and then copy that information to my new 3DSXL's SD card later and accomplish the same thing? I only care about "Find Mii" hats/titles and puzzle pieces. Thank you in advance for your help!
Having done a system transfer myself, I can say that all puzzle peices are kept intact.
Having not done a 3DS to PC backup myself, I can't give word on that. But Nintendo does really need to make a valid backup system, seeing as they aren't moving toward a unified account system any faster.