How to reproduce:
1. Open the submitted project
2. Drag the Cube GameObject from the Hierarchy to the Project window to create a Prefab Variant
3. Delete the Cube Prefab
4. Select Cube Variant Prefab in the project window
5. Inspect the Root in Prefab Asset menu in the Inspector window

Expected result: Root in Prefab Asset menu displays only the Transform Component
Actual result: Root in Prefab Asset menu displays all the deleted Components

Reproducible with: 2019.1.9f1, 2019.2.0b9

Notes:
Root in Prefab Asset menu was introduced in Unity versions 2019.1.0f2 and 2019.2.0a12, thus introducing the issue.
The issue does not reproduce with Unity version 2019.3.0a1 and above.
Changing parameters of non-existent Components will result in a Console error and a warning.
Until Unity versions 2019.1.7f1 and 2019.2.0b5, changing parameters of non-existent Components would override the Prefab and all the Components would get reattached.