Oops, I think I get what's happened now.
It's on how I use my back ups. When I load my back ups i simply open the world folder in the zip file and transfer all the files to the world folder in the saves folder, since the nether hasn't generated yet from my old save file, there will be nothing to overwrite the nether world in my saves folder so it will remain there unchanged.
Guess there's nothing left to this topic lol. Sorry.
I'll just delete the current save file that has doubled items in it.