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I wonder if this will work.
Digital version of Pokemon X and Y will most likely have Animal Crossing New Leaf's "save lock" in SD cards where you can't back it up (it doesn't even feature the 3DS's built-in back up feature).
However, what if you downloaded Pokemon XY in two different SD cards? One would be your main save while the other is for the miscellaneous run. You simply switch SD cards to play which.
