If that’s the case, you’ll have to play it with your full team on a real 3DS. In JK’s Save Manager (If you don’t have that installed, there’s a guide here.), Go to Pokemon Moon, export a save, and name it anything. Now, there should be a
JKSM folder on the root of your SD card, and in there a
Pokemon Moon folder (This is why I said to export a random save, to create this folder.). Copy your save from Citra into the
Pokemon Moon folder, and, from JKSM, import that.