Mind explaining how it works?
Called the customer support line, where there's a specific option to select to transfer content from one system to another. After this, I explained my situation to the rep and he asked me for my NNID and the serial number from the new 3DS. (He paused for a moment and said, 'Ok, let me your serial number from your old 3DS,'--I told him no need I had it written down.) He then restated back to me what I wanted him to do, which I confirmed for him. He then asked to verify by either telling him my Club Nintendo login or telling him a few purchases I had made on my old 3DS...he told me the more obscure the better, so I told him Shin Megami Tensei IV, a couple GameGear VC games and a few G-Style indie games. He said OK and then asked if I had DSiWare content tied to the console, which I did and he said OK, we'll recover that as well.
He restated my aim again, by saying "So you want to merge NNIDs and then migrate the old NNID to your new 3DS with ______ serial number, from your old 3DS with ______ serial number and the DSi content associated with it?"
I said yes, he told me I would receive an email within 24-48 hours detailing the last step I needed to take and to keep an eye out for that. I said ok, hung up and then ended receiving three emails shortly thereafter.
-One saying they were deleting my NNID
-A Second, about 2 hours later, saying that my issue had been resolved and to log back in.
-And a third asking me to take a survey, which I did.