Steps to reproduce:

1) User 1 creates a cube in an empty project and pushes through collab.
2) User 2 pulls the project. He adds a child sphere gameobject to the cube. So in the hierarchy now there is a camera, directional light and parent cube with child sphere.
3) User 1 changes the name of cube to something else and pushes the project.
4) User 2 tries to pull/update the project. Save the scene when prompted to save the scene. Reload the scene when prompted to reload. User 2 loses all data in hierarchy with unknown error.

Regression : no

Verirfied on : Unity 2017.3.b11, 2017.3.b9, 2017.2.f3.

License type: Free

Stack trace: Unknown error occurred while loading 'Assets/Scene/MergeTestScene.unity'.

Workaround : Right click the scene file in the project, Collaborate > Revert.