Take the sd out before formatting the sysnand and the emunand will still have all your stuff. Typically there is a package error when NANDs are linked. Meaning that apps get repacked into presents everytime you load the homemenu. Also with NANDs linked, if you go to the 3ds apps, say to delete something, in the settings menu it will remove all your nonlegit apps. That includes homebrew and pirated games. There have been a few reports of updating the emunand with rxtools while NANDs are linked and it updating the sysnand as well, or instead.
So boot the 3ds into sysnand, go to settings, remove the sd, and format the system. Restart it, go through initial setup, put sd back in and setup reinstall the exploit you use.
If you update emunand, go to system settings from emunand. Make sure your firmware version begins with rx-e. If not, then exit and try again. If it does, do NOT exit system settings. Instead go to other settings, then page 4 and update. You can only update emunand from system settings and only when the fw begins with rx-e. Rx-s means your in sysnand and will update the sysnand as well.
Hope that helps.
