while messing with #checkpoint for the #3ds, it looks like you can copy saves between carts and digital versions of the game if they're the same ID.
for example, I can copy save states between my eshop copy of #blazblue continuum shift ii and my cart because they're both the n.american id.
I can't however do that between my japanese cart of #kokuga and my n.america copy from the eshop. at least I don't think I can...