Instead of editing the alpha for each material, it would be quicker for me in this case to be able to fade out the entire render layer in the node compositor.
The "SetAlpha" node seems perfect for this, but it adds black to the alpha channel that I don't want. The background needs to remain transparent, and not be black.
Here is my simple setup (without the SetAlpha node). How can I fade the "bearing" render layer to zero opacity, leaving only the "freestyle" layer on screen?
Also, I should note that I can't just switch the inputs on the Alpha Over node and use the "factor" to fade out the "bearing" layer, because the "freestyle" layer needs to remain over the top of the "bearing" layer.