It's been awhile since I did it, but I think I was using these tutorials at the time, and I just dumped everything, even if it was claimed to not be used by Citra.
https://citra-emu.org/wiki/dumping-save-data-from-a-3ds-console
https://citra-emu.org/wiki/dumping-extra-data-from-a-3ds-console...