Here's what you have to do. First, make sure that you do not have the Ray-traced renderer turned on. Second, pre-compose your multiple layers. Third Collapse transformations. Fourth, add a new 3D layer using a red or blue solid with the blend mode set to screen and position this layer so that it will cover the entire pre-comp. Now, and this is the reason for the screen blend mode, use the pen tool to draw your mask on the layer then set the layer as a track matte for the pre-comp. Animate the matte and you're done.
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