I'm not completely sure that this will work, but it might work.
If I'm correct, system transfer completely moves all of the data.
If you have an SD card reader, put the SD card for your current 3DS (the one with X) into the reader and plug it into your computer. Save the files to the computer then remove the SD card reader from your computer. Put your SD card back into your 3DS and do the system transfer. (If I'm correct on how system transfer works, it completely moves ALL of the data and you only want Pokemon X moved.) After the transfer, put the 3DS SD card into the SD card reader, and put the SD card reader back into your computer. Now copy the files that you previously uploaded to your computer to the SD card.
If it works, each 3DS should have the exact same data, you may have to delete some stuff on the New 3DS, but it's the only way I could think of.
(note, this may not work!)