BY DESIGN:
The reason for this flickering is batching. All geometry using specific shader flickers due to it using object-space data in the shader, which was lost when geometry was batched.
To avoid that, add DisableBatching tag to the shader affected. https://docs.unity3d.com/Manual/SL-SubShaderTags.html

To reproduce:
1) Import attached Unity Package
2) Open Maps/MapA scene
3) Play it
4) Switch to Scene View
5) Try moving around

Expected: The lighting stays the same
Actual: The lighting flickers erratically as you move and sometimes persists even after move

Reproduced in 5.5.0f2, 5.5.0p4, 5.6.0b4