To reproduce:
1. Open project attached by the QA
2. Open "Main" scene if not opened
3. In hierarchy window select "Plane" game object
4. Find NavMesh Surface component and bake it
5. Enter play mode
6. Enter scene view and notice that NavMesh Surface baked area has disappeared
7. Exit play mode and notice that there is no baked area on the Plane

Expected: Baked area shouldn't disappear after entering play mode.
Actual: Baked area disappears.

Note: This happens only with prefabs and if baked area is cleared on the prefab.
Workaround: Bake area within prefab.

Reproduced with: 5.6.2p2, 2017.1.0f2, 2017.2.0b2
Wasn't able to test on 5.5.x versions because of errors.