So I just discovered this: "SSB4 Manual, page 7 About the Downloadable Version If you have your save data on an SD card and try to overwrite it with save data you previously transferred to your computer, the Nintendo 3DS will not be able to read the save data. It is not possible to back up your save data this way, so please keep this in mind." So this basically means it is pointless to backup the save file as it wont be readable. Have tried multiple times to copy my saved file across and just wont work. If its in the manual then I suspect this is permanent and they will not release a patch to resolve this issue as it's an intended feature? This sucks.