Ok, I had a similar problem. I wanted to transfer a broken 3ds to a good new 2ds. The problem was: The broken 3ds turned of sometimes and it did again while the transfer was going on. So ofc it didn't work. How I fixed it: I toke the 2ds (so the target system), and formated the sd card. Then I hacked the 2ds. (Installing cfw). After this was done, i toke the sd card of the system I wanted to transfer, and copyed the sd card, the pasted it to the target sd card. After this was done, i put the target sd card in my target system, then I opend Godemode9 by pressing power and start. Navigate to: press a---sd---gm9---out---backup nand (should be called something like"numbers-numbers_sysnand_00.bin", not the bin.sha)---nand image options---restore sysnand---then press the button code that will be shown---now wait, it will restore your 3ds, but on your new system---press a 2 times, then start, to reboot your console
If everything worked: Congrats, you succsesfully transfered your sytem
If you find it hard to follow me, you can use this video:
(18) CLONING EVERYTHING FROM ONE 3DS TO ANOTHER : GO WILD! - YouTube
Simply do everything, sthetix does for the sytem that gets cloned, for your target system
I hope I could help, let me know if something went wrong or you need more help