Hello and sorry for the late reply!
Can you please let me know the exact steps to reproduce this problem?
This is what I have tried and seems to not reset the variables:
1. I created a prefab asset (with a blackboard) and added some variables.
2. I create a prefab variant from that prefab asset in the project (right click -> create -> prefab variant) and added some extra variables.
3. The original prefab’s variables are not reset on the variant and seem to be retained.
Using Unity 2018.3.0f2
Please let me know of the steps to reproduce!