[Seth Carper] “*Added note: I’m not sure the cause of this, but it appears that this invisibility effect (if you want to call it that) appears only within a section of layers in my composition. It is not a feature of the layers themselves. example: as a test, I created a new layer low in the layer panel; and it was invisible as the others. I think dragged that layer to the top of my layer stack in the composition, and it was completely visible (as are all others above a certain point in the composition). That seems very strange to me. . . “
It might indicate that there is an adjustment layer or an effect applied to a layer below which layers are not visible. Can you identify at what layer index other layers become invisible?
Slightly OT, at over 500 layers the Composition becomes somewhat unwieldy. Have you considered Pre_composing some sections and nesting these in a Master Comp?