I had this problem when I was transferring 3DS to New 3DS, the problem here is that the game doesn't save to the cart is actually saves data to the exdata if I remember correctly, I found a tool here "https://www.dropbox.com/s/yz7n3a49ylmjp3g/FLsavetool.zip?dl=0" Linked to from this page "https://gbatemp.net/threads/release-fantasy-life-save-viewer-editor.374495/". I ran it on one 3DS to extract the data, copied it to the SD card of the New 3DS and then ran it to import the save, whole thing took me about a minute, really handy homebrew. Hope it helps