Hello, I think that this isn't correct behaviour of Prefab variants, or I'm mistaken? Steps to reproduce: 1. Create a cube 2. Create a Prefab from the cube 3. Change the cube prefab's name and delete any component on it 4. Create from the cube Prefab variant 5. Change the cube in the scene 6. Press Apply all Result: On the cube, the previously deleted component appeared and in the project window the prefab variant changed to the scene state. Expected: Apply all adds changes made in the scene to the prefab variant in the project window.