Thank you so much! I used this to unlink my old NNID so I could link a Pretendo PNID without having to create a new wiiu user and transfer my save files between.
You can actually make the account act like it has no NNID and remove it directly from the user settings as normal, which should also remove most left overs from the account.
Just open /storage_mlc/usr/save/system/act/USER_ID/account.dat and...
Yeah you can do this, Pokemon Home only cares about the game's save being in the system, as long as a save data is present you can extract and inject the save into the sysnand without the need of having access to the game.