Okay, let me try to clarify. The original post was written kind of late at night for me.
In my thoughts:
Graphics = Graphic files contained in the folder.
Sprites = Graphics added to the atlas itself.
I had a number of sprites that were no longer needed in my Atlas.
So, I deleted each unwanted sprite out of it, then saved. I was not aware there was a way to save the atlas
without saving the project itself. After I deleted the sprites, I wanted to add one more graphic to the atlas.
The new sprite was added to the atlas successfully.
However, when I created a UISprite object within the GUI, and selected the new sprite in the atlas, it does not show
in either the Editor or the Game View - with or without Play enabled. In effect, no new UISprite objects can be placed,
while the old still retain their sprites correctly.
I am currently using NGUI Version v3.5.3.