I'm searching for a stop-gap solution to the problem described in these posts:

http://answers.unity3d.com/questions/7971/prefabs-workflow-changing-models-in-a-3d-app-after-they-have-been-used-in-a-pre

http://answers.unity3d.com/questions/27884/updating-a-prefab-fbx-or-animation-while-using-version-control-is-broken

Our artist is in the process of adding/removing bones to fit budget, and we don't want to have to go through the prefab creation process every time changes are made to the mesh. My hope is that I can write a script that will instantiate the necessary game objects from an FBX imported character model, the move these objects directly into an instance of our "character template" prefab.

I'm able to instantiate the mesh and move all of its children into the prefab, but when I do so, the skinned mesh does not animate. References to the animation field of our animation-handling component don't fail or throw warnings. Weirder still, when the root game object (with skinned mesh and bone transform hierarchy children) is selected and anything that changes the object's state is triggered from the editor, animations start working. For example, if I play an animation on the mesh from the animation viewer, or even just check and uncheck an inspector property on the Animation component, the driver we're using to determine which animations should play activates and functions correctly.

To explain a little more concretely:

We have a prefab in our library called Character_Prefab. This prefab has a bunch of gameplay and networking scripts attached to it, and no game object children.

We also have a mesh in our Art directory that we'll call Character_Mesh.

I've attached a script to Character_Prefab that takes has one inspector field, a transform that is supposed to point to the character mesh you want to appear on the prefab when it is created. In this case, this transform is the Character_Mesh object generated from the FBX import.

The small bit of script that executes this is as follows:

void OnEnable()
{
    if(!_instantiated && gameObject != null) {
        if(_modelPrefab == null) {      
            log.Error(
                "ModelPrefab hasn't been assigned a prefab! Please assign a mesh prefab to this character prefab's SpawnMesh component!"
            );
        } else {

            Animation animationComponent = gameObject.GetComponent<Animation>();
            if(animationComponent == null) {
                log.MissingComponent(typeof(Animation));
            }

            Transform newMesh = (Transform)Instantiate(_modelPrefab, Vector3.zero, Quaternion.identity);
            newMesh.parent = gameObject.transform;
            newMesh.localPosition = Vector3.zero;

            // Create a list of the children we need to move. Setting child.parent to a new
            // value while iterating over the list seems to cause us to miss some elements.

            ArrayList children = new ArrayList();
            foreach(Transform child in newMesh) {
                children.Add(child);
            }

            // Move them.

            foreach(Transform child in children) {
                child.parent = gameObject.transform;
            }

            print("Prefab animation component = " + newMesh.animation);
            print("This animation component   = " + animationComponent);

            // Delete the prefab object.
            DestroyImmediate(newMesh.gameObject);

            _instantiated = true;
        }
    }
}

The class is also set to trigger OnEnable when the prefab is dragged into the editor scene window via the [ExecuteInEditMode] metadata tag, but I don't imagine this is part of the problem.

My hypothesis is that some internal state variable isn't being updated to notify the Skinned Mesh Renderer that the Animation component has changed. Normally, were you to drag the FBX-imported mesh directly into the scene, it would begin with an Animation component attached to the parent object. In my case, this component is being abandoned in favor of an Animation component that already exists on our Character_Prefab prefab. When I change something in the editor, that might trigger a "hard" reset on a bunch of the objects such that the change is propagated. This syncs everything up and permits the animations to influence the skeletal transforms. However, the animation field of the Component object is read-only, so I can't simply assign the mesh object's animation field to the "real" Animation component. Also, kludgey efforts to replicate the "reset" via state changes post-mesh-instantiation (setting a boolean to one value on update 0, then back on update 1) don't seem to trigger the "fix" I'm observing when I make a change in the editor.

That being said, here's the crux of my question:

Does anyone know what might be changing in either the Animation component, the Skinned Mesh Renderer, or the game object hierarchy when I make an adjustment to the instantiated game object via the inspector, such that animations start affecting the bone transforms? Or for that matter, tips/tricks about spawning a skinned mesh onto an existing prefab containing an initialized Animation component?

Alternatively, I was thinking it might work if I leave the instantiated prefab intact, parent it to the prefab with game logic scripts, and adjust all of our game logic scripts to compensate for the object hierarchy change. I'd rather not do that, but if push comes to shove, it would be an acceptable-ish solution.

Thanks in advance for any help and/or suggestions!