Combined Mesh is lost from MeshFilter after applying changes to prefab in Playmode

To repro:
1. Open Project attached.
2. Open NightTime Scene.
3. In Hierarchy select Highway -> Bridge_ToStreet_Double_Exit.
Note: MeshFilter of this object is Bridge_ToStreet_Double.
4. Press Play.
Note: MeshFilter of this object is now Combined Mesh (root: scene).
5. Change Transform -> rotation of selected object (e.g. x = 0).
Note: Only Mesh is rotated.
6. Press Apply.
7. Exit Playmode.

Actual result: MeshFilter is lost for this object and all other instances of this prefab.
Error in Console: InvalidOperationException: This cannot be used during play mode.
UnityEditor.SceneManagement.EditorSceneManager.MarkSceneDirty (Scene scene) (at /Users/builduser/buildslave/unity/build/artifacts/generated/common/editor/EditorSceneManagerBindings.gen.cs:147)
UnityEditor.GameObjectInspector.DoPrefabButtons (PrefabType prefabType, UnityEngine.GameObject go) (at /Users/builduser/buildslave/unity/build/Editor/Mono/Inspector/GameObjectInspector.cs:355)
(related case 839122).

Expected result: MeshFilter stays on object.

Versions info:
There is no ability to apply changes to prefab in 5.3.6p5 (28930307ad49).
Reproducible in 5.4.1p3 (1b587b7935dc) and 5.5.0b7 (bd91e53964bc).