You'll need to manually unlink emunand and relink since you unlinked NNID in sysnand. This removed your console from Nintendo servers so emunand won't connect to your NNID anymore.
The only way to fix this is to relink emunand. (you can't relink sysnand now because it will ask you to update it). You can do that without formatting emunand I believe. Just delete the system save game for the act module which is where NNID info is stored. use rxtools to extract ctrnand.bin from emunand (make a backup before you do this). Then use WinImage to edit the decrypted FAT16 file. You should delete the the save game for act module located at Data\ID0\000202C0 for USA consoles.
If you don't use a USA region console the save game will be in a different folder. I've listed the 2 other possibilities below:
Japan:
Data\ID0\000202BF
Europe:
Data\ID0\000202C1
"ID0" is the folder which file name is a long string of letters and numbers. It's file name is generated via movable.sed file in the private folder so it is unique to your current configuration and will not have the same file name on other consoles.
Once the file is deleted reimport ctrnand and setup NNID again. If it still doesn't work, you may also have to delete save games for system settings and config. Refer to this site for information on where they will be located:
http://www.3dbrew.org/wiki/System_SaveData
Note that if you have to delete the save game for config the console will behave as if it was formatted next time you boot it. It will ask for language and you would go through the setup menu as if it was reset. Don't worry though, your current friend code and all associated software is still present. The only thing you lose is your primary Mii (and perhaps any other Miis you might have made in Mii Maker). But everything else will still be there.
If you don't want to go through all that, you can backup emunand, transfer sysnand to emunand, update it through system settings, then relink NNID. Then restore your emunand backup. The linked NNID in your emunand will work again.
