[MSE::Save] Deleting a scene from assets and saving it back from Hierarchy throws exception

Steps to repro:
1. Open the attached project
2. Double click on scene 1
3. Add scene 2 and make a composite scene
4. Delete scene 2 from the assets folder
5. Now save scene 2 from the hierarchy view

Note that an exception is thrown in the console as follows:
Asset '/Users/harini/unity/build/MacEditor/Unity.app/Contents/UnityExtensions/Unity/UnitTestsRunner/Editor/nunit.framework.dll' is in timestamps but is not known in assetdatabase...
UnityEditor.EditorSceneManager:INTERNAL_CALL_SaveScene(Scene&, String, Boolean)
UnityEditor.EditorSceneManager:SaveScene(Scene, String, Boolean) (at /Users/harini/unity/artifacts/generated/common/editor/EditorSceneManagerBindings.gen.cs:109)
UnityEditor.GameObjectTreeViewGUI:DoAdditionalSceneHeaderGUI(GameObjectTreeViewItem, Rect) (at /Users/harini/unity/Editor/Mono/GUI/TreeView/GameObjectTreeViewGUI.cs:137)
UnityEditor.GameObjectTreeViewGUI:DoNodeGUI(Rect, Int32, TreeViewItem, Boolean, Boolean, Boolean) (at /Users/harini/unity/Editor/Mono/GUI/TreeView/GameObjectTreeViewGUI.cs:106)
UnityEditor.TreeViewGUI:OnRowGUI(Rect, TreeViewItem, Int32, Boolean, Boolean) (at /Users/harini/unity/Editor/Mono/GUI/TreeView/TreeViewGUI.cs:191)
UnityEditor.TreeView:DoItemGUI(Int32, List`1, Single, Boolean) (at /Users/harini/unity/Editor/Mono/GUI/TreeView/TreeView.cs:406)
UnityEditor.TreeView:OnGUI(Rect, Int32) (at /Users/harini/unity/Editor/Mono/GUI/TreeView/TreeView.cs:516)
UnityEditor.SceneHierarchyWindow:DoTreeView(Single) (at /Users/harini/unity/Editor/Mono/SceneHierarchyWindow.cs:364)
UnityEditor.SceneHierarchyWindow:OnGUI() (at /Users/harini/unity/Editor/Mono/SceneHierarchyWindow.cs:197)
System.Reflection.MonoMethod:InternalInvoke(Object, Object[], Exception&)
System.Reflection.MonoMethod:Invoke(Object, BindingFlags, Binder, Object[], CultureInfo) (at /Users/builduser/buildslave/mono-runtime-and-classlibs/build/mcs/class/corlib/System.Reflection/MonoMethod.cs:222)
System.Reflection.MethodBase:Invoke(Object, Object[]) (at /Users/builduser/buildslave/mono-runtime-and-classlibs/build/mcs/class/corlib/System.Reflection/MethodBase.cs:115)
UnityEditor.HostView:Invoke(String, Object) (at /Users/harini/unity/Editor/Mono/HostView.cs:187)
UnityEditor.HostView:Invoke(String) (at /Users/harini/unity/Editor/Mono/HostView.cs:180)
UnityEditor.DockArea:OnGUI() (at /Users/harini/unity/Editor/Mono/GUI/DockArea.cs:336)
[/Users/harini/unity/Editor/Src/AssetPipeline/AssetDatabase.cpp line 592]