You mean save files, correct?
Please remove all homebrew files from your SD card, and try this method.
https://smealum.github.io/ninjhax2/starter.zip
Place the contents of the
starter folder on the root of your 3DS's SD Card.
https://github.com/J-D-K/JKSM/releases/download/6-30-2016/JKSM.6-30-2016.zip
Then, download this and place the
3ds folder on the root of your 3DS's SD Card.
Then insert the SD card back into your 3DS.
Then open your 3DS's Internet Browser to this page:
http://yls8.mtheall.com/3dsbrowserhax_auto.php
Or scan this QR code with the home menu QR code scanner to open it.
From there, open the Homebrew Called JKSM (or JK's Save Manager)
with that tool, you can make backups of any save file you want, or restore backups of any save you want. For reference, the "cartridge" option is the one you use for any game you have inserted into the 3DS.
Save files will appear in SD:/JKSM/Saves/ after this.
In addition, new folders can be made containing complete save files inside a game's folder for restoration.
If you have one of the
secondary exploit games, I recommend installing the exploit to one of your games for more future proof 3DS homebrew access, as browserhax will likely be patched again on the next Firmware Update.
At this time, more complex hacking (cfw and other arm9 homebrew) is not possible on 11.0 systems. (yet... who knows what the future holds?

; )