Prefab loses reference to a scriptable object

Hello,

We are experiencing an issue while using symlinks that our character prefabs loose a reference to a shared scriptable object asset on a build server. The problem is that the lost reference is shown as None, but reassigning it back to initial value doesn't trigger git changes which means that the reference somehow is still recorded internally without stating Missing reference. But assigning to some other value, including None does show the change. I wonder what kind of missing reference is that and how to avoid it.

This is a blocking issue, so thanks a lot for any ideas beforehand!