How do I keep from losing the color when I "Convert Shapes from Vector Layer" in AfterEffects? I often design everything in Illustrator, then import the file into AfterEffects as a composition, apply "Convert Shapes from Vector Files" to each layer so that I am working with vector, and then animate the new shapes. 

However, I just ran into an issue where I convert a compound shape (with solid color), and after I apply "Convert Shapes from Vector Layer", it shows up as transparent. The layer is there, and I can modify the vector points, but I don't see it.  When I click on the shape, it still shows white in the Fill. Opacity is at 100%. 

Any thoughts?
It could be another path within that layer in the Illustrator file. Check there first and make sure there isn't a mask of any kind.

You can also try looking in the layer within After Effects, click the Contents dropdown, and then the Group dropdown, and check for another Group under your paths. If you see another Group, change the visibility for the Group to see if your shape color returns.