Steps:
1. Open attached project
2. Make a variant ("Variant") out of any GameObject in Hierarchy
3. Add another GameObject ("GameObject") to Hierarchy
4. Add "TestScript" script to "GameObject"
5. Assign "Variant" prefab instance to a reference in "TestScript" component in "GameObject"
6. Save the scene
7. Move Parent prefab asset out of the project with corresponding meta file via OS
==> "GameObject" lost reference to a "Variant"
8. Move Parent prefab asset with its meta file back to the project via OS
==> Reference is still lost

Also reproducible: 2020.3.27f1