Hello, from what I can find citra uses the exported save files correct? If so it should be doable, so I'll get the game and attempt to export it using JKSV. I'll sent you a PM to let you know whether it worked or not.
So a quick update, there might be something wrong with the save. I've tried multiple times with both JKSV and savedatafiler, and both of them give an error with this particular save (saves for other games do work so I'm pretty sure that my 3ds is not the issue).