I'm not very experienced with editing and hacking, so I'm sorry if I wasn't clear enough, lol. And I'm sorry if I'm misunderstanding your question, so please forgive me if I'm saying things you already know.
You'll need to have two backup files. One that is older, that will have all your villagers. If it's on your 3DS right now, you might want to copy it over to your computer before making a new backup, in case it gets overwritten when you backup a new one.
The other file is brand new, made for the purpose of grabbing the NAND.
On the
ACNL save editor, on the last tab, you'll see 'secure value' under the Town Info. This is your NAND. The NAND from your old file will not work if you tried injecting it. Click the pencil icon next to the secure value code, and it'll bring up a box that basically says what I have (oops).
Click on the red button, and grab the NAND from the brand new backup. It automatically changes it. Save the updated file, and you should be able to succesfully inject and open it on your console.