I don't fully understand your issue, but what it sounds like is that when you fully prep your app for publishing in the app store, it creates a duplicate entry in the manifest file.
If my impression is correct, then try manually removing the line that you see when you said "I Checked Before Enhancing And There Is Only One Line", then maybe when you are using the "Enhance Extension", it will add that line as you've seen, but now there will only be one line in the manifest.