Hi folks –
I had a similar problem creating an After Effects composition from an Illustrator logo. I imported the illustrator (.ai file) in to the After Effects as as a composition (retaining layer sizes) and at first everything worked fine and I was able to animate the logo. I’m using Adobe Creative Suite CS6 on an iMac.
However, I came back to the After Effects project today and one of the layers appeared to had vanished. I checked the Illustrator file and it appeared to have vanished as well. So, I clicked the layer in Illustrator that was not showing up and inside it I double clicked the icon of the logo next to . When you do this a dialogue box popped up and it has two click boxes “Show” and “Lock”. I clicked show and the layer was showing again.
After restarting After Effects, the layer also showed up in that program and all was resolved. Hope this helps.