I believe that you can only clone your source 3DS's digital contents + NNID by
(1) Backup source emuNAND,
(2) System Transfer,
(3) Restore source emuNAND backup,
to make several 3DSes shared the same digital contents & NNID, isn't it?
Since Nintendo only recognizes NNID on the latest System Transfer target, your previous sources are definitely unable to use that NNID otherwise all your ticket (=digital content's identification) one that clone should be wiped out.
If you want to use your cloned digital contents with a brand new NNID, I think you may need to register it on a new emuNAND, then manually move the new NNID data to replace old NNID data. (Need emuNAND decryption & modification)
Since your new NNID doesn't have any ticket, your cloned digital contents should be wiped out unless you never connect it to the Internet or prepay everything on your new NNID before moving it.
If you do not want to use your cloned digital contents on a new NNID, just use a new emuNAND to register it.
Your 3DSes, which store your old clones, should be NNID-free that is able to be registered any new one.