Hacking About to system format emuNAND, need a little help.

[Treeko]

Alright I am about to system format emuNAND to link my NNID to it, unfortunately while setting emuNAND I didn't know that you have to re-link NNID to access eShop in emuNAND, after the system format would I lose stuff like the cia's I've installed and BigBluemenu? just to be on the safe side....