How to reproduce:
1. Create a new project
2. Create a Cube GameObject and an empty GameObject in the Scene
3. Drag the Cube GameObject to the Project window to create a Prefab
4. Delete the Cube Prefab
5. Rename the empty GameObject to Cube
6. Drag the empty GameObject to the Project window to Create a Prefab
7. Inspect the original Cube GameObject

Expected result: The GameObject with broken Prefab connection does not change
Actual result: The GameObject with broken Prefab connection overrides its connection

Reproduced with: 2018.4.3f1, 2019.1.9f1, 2019.2.0b9, 2019.3.0a8

Notes:
Notice that the override will cause the GameObject to change all its Components and their settings.
The issue does not reproduce if the project is reopened after step 4.