Plug your SD card into your PC and go to this location c:\"Your SD card location"\Nintendo 3DS\"your Sysnand ID"\title\00040000\xxxxx.
The xxxxx is the games individual ID which you can google for, If its an american monster hunter 4 ultimate then the xxxxx = 00126300. The save will be in this folder in an encrypted format which can be then injected into card 2 .3ds and well nothing much else unless the game has a save editor for it that has been publicly released.
If the games Cartridge reads the games save from the SD card (card 1) then you may be able to use the eshop save for the retail cart version, but if it saves to the cart(card 2) then sorry but there isnt much you can do.