I have a plan that I will be executing in a few weeks, and I want to make sure there are no flaws in it. Basically, I don't want to risk losing my village! I am buying the Zelda 3DS XL, and I anticipate it being my main 3DS. As such, I plan to transfer everything over to it from my current 3DS. Once I transfer, I would like to buy the download version of AC (I have the cartridge now), use the save transfer utility to send my village to the download version, and then I will use the cartridge to create another town on my original 3DS. That should work fine, right? I can then visit my other village, trade villagers, streetpass myself, etc. At least, I assume that's all possible. It'll be great having the download, because I haven't taken my cartridge out since July and thus haven't played anything else except for games I've downloaded.
Are you saying you want to transfer the save data on your cartridge to the downloaded copy? That's not possible. The DL copy will have to be your new town. You can play your old game in the same 3DS though -- and just use the old 3DS when you need to travel back and forth.