Did you ever find a work around for this? I am in the same situation. I’m creating 3D boxes out of Photoshop layers in AE. When we get new box designs for the client, I need to replace the layers (relink each one by one) in the AE project file. One or two at a time isn’t an issue, but I’ll regularly get 20+ designs, each with 6 layers to replace. The time adds up very quickly.