So it is possible to transfer pokemon from and to a 3ds? Man this was done rater quick. Really want to try this out!
Probably going to test this using a Virtual Machine, don't want to screw up my settings and such.
At the moment you are not transferring anything. In short all you are doing is watching the pokemon trade on the computer. You can take a copy of this transfer data (including the pokemon in the data). Extract the pokemon data so you have like the current .pkm files but for x and y.
You only watched the trade happen and between the 3DS and other 3DS the trade did happen for real so everything on 3ds is how it should be nothing new.
What you do with the data and pokemon when its on your PC is the next step to work out. No one knows how to trade it back all attempts have failed.