This is based on a problem I recently encountered and may not apply to people who are smarter than I am.
When you have a complex scene and you need to turn off the visibility of some layers, don't turn them off by clicking on the eye symbol in the layers palette. If you do that and forget to turn the visiblity back on again, the layers won't render. Instead use the "Hide in editing view" option under the "Current Layer" pop-up menu in the timeline. This is something that's easy to overlook, so I thought I'd mention it.
As an example, I had a character whose face was in shadow. I made a shadow shape, set its color to black, made it a bit transparent and set its transfer mode to "multiply". However, since it covered the character's face I had to turn off its visibility in order to animate the facial features. I had rendered out my animation several times, after doing many fixes, before I realized that the shadow layer wasn't rendering because I had forgotten to turn the visibility back on, so I had to render those scenes all over again.
(LM, if you're reading this, I suggest that turning layers on and off in the layer window shouldn't affect their visibility when rendering. For that there is already the layer visiblity check box in the layer properties.)
Layer visibility tip.
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