When it ended the transfer and said "The system will now restart" on the original 3DS, did you hit OK, and then removed the SD card? I've heard if you don't move the SD card until after it's formatted you lose your games.

The 3DS itself will tell you to "move the SD card to the new system now" at some point during the transfer, if I remember correctly.

The only problem I can think of would come from inserting the card on the new 3DS before You're told to, that will format it.

Hmm... Well I looked up on youtube a video of the transfer and it seems that the 3DS XL asks you that, while the other system says it'll restart... Then the guy lost his data.

If you don't feel confident enough, just back up your data on a computer or something.

I can tell you that nothing happened to MY data and all I did was follow the on-screen instructions, if that makes you feel better.

That is why nintendo recommends to backup your SD cards before you begin the process.

How do I back up the SD cards on my computer?

1- insert SD card on computer
2- open SD card with file explorer
3- select everything
4- copy it all
5- create a new folder somewhere else (meaning: not on the same SD card)
6- copy everything inside that folder
7- ???
8- success!

mine was simple because I actually have a SD card slot built-in to my laptop but if you don't have that you can buy a external multi SD card USB box cheap these days.

I have a vivitar SD card reader for mac, so I'll use that. So should I make the new folder on the desktop, and name it 3DS stuff?

Yeah, that should work.

To use that back up in case of failure, just reuse the same SD card or a new one (you may need to format it) and copy everything inside that folder (meaning: not the folder itself) back to it.
The 3DS will be able to read it all.

yeah that's pretty much what I did and I still have that folder on my PC and update it every 2 months or so as a precaution just in case I need it for a rainy day

Well, all right. Should I do it for both? I'm planning on using my 2 GB that came with the system for the transfer, as I don't really care about anything on that card besides streetpass. But after the transfer I'm planning on putting in my 8 GB after the 2 GB is done.

If you have an SD card reader, you can copy and paste EVERYTHING from the 3DS SD card. This copies ALL information tied to your 3DS. When you transfer systems, that information will be transferred, allowing you to keep everything, INCLUDING your downloads and saved data. Then reinsert the SD card.

You only really need to backup your main one, but I guess you can keep backups for both if you feel like. Just remember not to mix them.

Oh yeah, another thing: even though I'm not interested in doing this, but is there a way to combine both SD cards?

I don't really know, I guess just merging them (copy the contents of one on another)?

You can try it once you have the backups, that way nothing is lost if it doesn't work.

Hm... Then I'll refrain from that. I'll just now have to get a XL ASAP (Hopefully tomorrow )