Hello guys. I want to let you know that this edge case issue of cycle referenced blackboard prefabs when the Library folder is deleted, is fixed.
The problem was in serialization rather than deserialization. This fix is the following piece of code added at the start of the ‘SelfSerialize’ method in Blackboard.cs
//This fixes an edge case of cycle referencing prefab blackboards when the Library folder is deleted
//which was basically due to the prefabs being serialized before the database was re-built.