Format sysNAND.

 

Okay so you are gonna need to get EmuNAND Tool (Google it its on here somewhere)
Then extract your EmuNAND then reformat EmuNAND (Google Search TinyFormat for 3DS It won't delete your SD Card Items)
After reformatting go through the entire setup process
Now with that EmuNAND log into your NNID

Now power down and Re-Inject the NAND back into your EmuNAND partition and it should all work fine
(If you get an Invalid NAND Size error download the 1.0.1 Version of EmuNAND Tool)

 

I presume that this is what you did, right?

 

Yes

 

It Formats your EmuNAND without formatting your SD

 

Nevermind i've fixed my issue i formatted my emunand though system setting and that let me link my nnid to my emunand one more question does emunand have my friend code inside of it since i did do a backup before i formatted my emunand

 

You just have to make an emunand backup and a backup of your nand's folder in sdmc:/Nintendo 3DS/, then format emunand in system settings, re-link your NNID in your newly formatted emunand, then restore emunand backup and restore your folder in Nintendo 3DS so you don't lose your games and your saves.

use EmuNAND Tool (Google it its on here somewhere) to make the emunand backup

that's what i did.

 

I would make another emunand backup using EmuNAND Tool just to be safe you can also use that to restore the emunand backup that's what i did
You just have to make an emunand backup and a backup of your nand's folder in sdmc:/Nintendo 3DS/, then format emunand in system settings, re-link your NNID in your newly formatted emunand, then restore emunand backup and restore your folder in Nintendo 3DS so you don't lose your games and your saves.

 

Once you've formatted the emunand and linked your nnid make sure you format the emunand though the system settings inside emunand but before that make a back up of the emunand using the EmuNAND Tool

 

Have you linked your nnid to the new emunand?