When replacing a prefab asset the transforms, as well as all modifications to all prefab instances in the scene of that prefab asset, are reset.

Steps:
1. Open user's attached project ("Nested Prefabs Beta Bug Report.zip")
2. Open the "SampleScene" scene
3. Notice: there are two prefab instances in the scene of the "Prefab" asset. The first instance is named "Prefab", the second instance is named "Another prefab instance of the same prefab". "Another prefab instance of the same prefab" has a modification to the Rigidbody component: the mass is set to '5'. It also has a different position (x=1, y=2, x=3).
4. Drag the prefab instance named "Prefab" onto the "Prefab" asset in the project window to replace it

Expected: "Another prefab instance of the same prefab" is not modified.
Actual: "Another prefab instance of the same prefab" gets values of "Prefab".

Reproduced with: 2018.3.0a6, 2018.3.0b3, 2019.1.0a2.
Not reproduced with: 2017.4.11f1, 2018.1.9f2, 2018.2.8f1, 2018.3.0a5.

Note: the bug appeared with the introduction of Nested Prefabs.