No, it will not. The Alpha layers need to be present in order for the window to be transparent.
Not sure what program you are using, but the Alpha layer is not visible as a normal layer. In Photoshop, you need it, to see it.
As long as the numbers are in the alpha layer, the transparency will make it to reappear. You will need to "erase" them there. Make sure the whole window is the same color in the alpha layer.