[UPDATE] I experimented and found out that the problem was caused by the .meta files changing what ID number it assigns to the root node. I'm guessing that means that this problem only applies to people using external version control? We'll be changing to the Unity Asset Server soon, and can try testing to see if this is still a problem.
We noticed a problem where when we updated an asset by reexporting the FBX from Max, that all the links to that object were broken. Is there a way around this?
I'm not sure if this is related or not, but we had to change the material generation method to be "per material" in order for the materials to update properly.
Here's a more detailed explanation of how the asset is linked. I have an Asset A, which is just sitting in some asset folder. I then create a Prefab P. I attach a script component S to P where S has a public GameObject member called AssetTemplate. I then go and link the asset A to AssetTemplate under the prefab and everything works fine. However once I make a change to Asset A, all of a sudden AssetTemplate under the prefab is now pointing to "Missing".
When you attach a script to the object, this object lost its link to the prefab (you can apply the altered settings to prefab) and lost its link with FBX "Tree".
So, when you make any change to model, in your 3D application, and Unity reimport this model, it will apply the mesh modifications, but if you add or delete any mesh in the FBX it will not apply this change to your object, because he lost its link.
There's no way to prevent this, what I do is to add the scripts By scripts while testing, and lastly attach the scripts directly to the object when finish.
Sorry for my bad gramar. Hope can help you. Borgo