you could install a legit cia of Pokemon X (so the cia can be read in classic mode), then enter classic mode and use Save Data Transfer Tool to move the save from the retail game to the legit cia, and then, back in Gateway mode, use SaveDataFiler to extract the save from the cia and inject it to the .3dz rom.
Hey I know it's been ages since you've posted this, but I'm about to do this now and just to be clear, am I right in thinking that this is reversible? i.e. if I ever decide to go back to my retail cart, would I have any problems doing so?
I'd extract the save from the cia using savedatafiler, but how would I then put this save back on my retail cart? Would I need to buy cubic ninja to use NTR or is there another way?
Thanks so much dude.