found this on gamefaqs. i haven't tested it myself so take with a grain of salt:
I had a separate ambassador console and a main console I played all the time. I didn't want to lose my save data, Mii Plaza data, etc. on my main console but wanted to combine everything onto that main one. I ended up transferring from my main console to the ambassador console first. It kept my save data but added the ambassador games and Zelda: Four Swords to my e-shop, so I was able to redownload those. I then waited seven days and transferred everything back.
Wow, that's an interesting solution!
I noticed that there's no Nintendo Network ID linked to my old 3DS, which means the purchase history must be stored on the actual console. I tried to log on to it with my new ID but couldn't since it's already linked to the New 3DS. I wonder if there is some sort of workaround.