This bug is repeatable using Unity 2019.1.4f1. When I delete a prefab from the hierarchy, then use a statement to check if the object is null, it is regarded as NOT null. When I put the prefab back in the hierarchy, the first instance somehow still exists. This has caused problems in which I’ll try to update the score of my game, but the score increases 2x the value I enter, or 3x if I delete the prefab and reinsert it again, 4x if I do it again, etc. When I close the editor and restart, things are back to normal until I remove the prefab that first time, then we start all over again.
There are a lot of things that are unclear here. Are you deleting via code or via the editor interface? In Edit Mode or Play Mode? What do you mean by ghosting? What do you mean by putting the Prefab back in the Hierarchy?
If you believe there is a bug (and you seem to, since you marked this post as bug) please file a bug report with repro project and exact repro steps. We don’t track bugs via the forums, and unstructured descriptions of bugs are often too vague to be able to investigate.