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I have two cubes in the scene. The larger cube is made transparent by decreasing the alpha value, and contains a solid red cube inside. enter image description here

As seen in the picture above, the transparency works fine in the rendered view, but when I bake the textures in Cycles (using the Simple Bake addon) the larger cube looses its transparency and takes on a solid color. enter image description here

How can I bake the transparency/alpha value so that the larger cube is see-through?

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