So my plan is to transfer from my old 3DS to my 3DS XL (not the new 3DS). I just recently found my old 3DS, so it doesn't have a NNID associated to it but it does have some games on it.

I'm thinking that I could transfer from my old 3Ds to the 3DS XL but to do so I'd have to format my 3DS XL to go through with the transfer. I'd probably copy all the stuff before the format from my 3DS XL onto my PC (so I wouldn't have to re-download everything) then transfer from my 3DS to the XL. When I link my NNID would I get all the games I bought with the NNID from the XL and the games from my old 3DS?

  • As far as I know, downloads are not linked to your NNID, they're linked to your console. The system transfer exists for that purpose, so you can download on your new device what you bought on your old one.
    – Nolonar
    Mar 21 '15 at 0:19
  • If you update the firmware on your original 3DS, you will be able to create an NNID and your existing things will be associated with it. Having said that, try a System Transfer first.
    – Powerlord
    Mar 23 '15 at 18:24

So (I don't mean to link to myself here, sorry) this might help answer your question. It has more to do with NNIs than what I think you're looking for, but it should still help somewhat. But here is relevant data to fully answer your question:

  • Your Nintendo Network ID is tied to your software and/or additional content you have purchased and downloaded. (Meaning if you have an NNI, the purchases you make are not linked to your console, but your NNI)
  • What is retained (when you create a new NNI): All game licenses purchased prior to linking a Nintendo Network ID, funds added prior to linking a Nintendo Network ID, and all free software demos downloaded prior to linking a Nintendo Network ID. (Just proof that anything that you download with an NNI on your system is retained)

Recently I bought the Persona Q 3DS and transferred data from my 3DS to the Persona 3DS. When I transferred my data, everything I bought moved from my original system to the new system. But the reformatting process will remove anything on the target system having to do with another NNI. But... no NNI is technically ANOTHER NNI so... You say your games (on one system) aren't connected to another NNI, but if I were you I would back those up just in case.

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