Boot into CTR and load homebrew menu, this will load the homebrew menu in sysNAND, load tinyformat to unlink NANDS, everything in your sysNAND should move into emuNAND while making your sysNAND completely new, reinstall menuhax and give it something like the Yellow basic theme.
Once finished, boot into emuNAND via cakes of whatever CFW you have, if you have a yellow theme, it's sysNAND, immediately power off and try again, when you are 100% sure you're in emuNAND, then you're free to update it through system settings like you normally would without cfw.