Re: Missing After Effects Layers

In your Project Window, you should have a comp named the same as your Illustrator file (unless you renamed it, of course), and a folder named [COMPNAME] Layers. Open that folder and you should see all your layers from the Illustrator file. Right-click one, choose "Replace Footage > File..." and navigate to the new location of your Illustrator file. Make sure "Import As:" at the bottom of the window is set to "Footage."

Once you've selected your AI file, you'll get another dialog box. Under "Layer Options" select "Choose Layer" and from the pop-up select the layer with the same name as the one you originally selected in the Project Window. Hit OK and all the rest of your layers should magically relink and appear in your project.