Hello,
Sorry for the late reply and thanks for the video.
I can confirm that this happens on the latest version of Unity 2018.3.6f1, while it does not happen in for example version 2018.3.0f2 …
Thus, aparently, Unity is still changing things as far as the new prefab system and their serialization goes to a point that it gets anoyingly inconsistent unfortunately :/ . I need to dig into this some more and find what could be causing this, or if maybe its a Unity bug introduced in latest Unity version, because the Blackboard serialization if actually very simple, just using the Unity OnBeforeSerialize and OnAfterDeserialize callbacks. Nothing really fancy.
