What I would recommend is:
1.) Use EmuNAND9 to clone sysNAND to emuNAND.
2.) Boot a CFW into sysNAND mode, install TinyFormat here, and format sysNAND, effectively swapping what they are right now.
(OPTIONAL) 3.) Install arm9loaderhax so you never boot into sysNAND again, just emuNAND!