Just use Emunand9Tool. It even can convert a EmuNAND to RedNAND.
there is close to 0 benefit doing this, especially if you want to save space on a New 3DS. to gain all the benefits of RedNAND, you need to create a RedNAND partition from scratch using EmuNAND9's Complete RedNAND setup.
afterward, you are free to restore an EmuNAND backup.