To reproduce:
1. Open user's attached project
2. Check Canvas Inspector window > Test One script component > Sprite Prefab field (make sure it's empty)
3. Enter Play mode - Sprite from Atlas is rendered
4. In Project window, find Atlas_A_Sprite_Prefab (Assets/Resources)
5. Insert Atlas_A_Sprite_Prefab into mentioned Sprite prefab field (2nd step)
6. Enter Play mode

Expected: Sprite is loaded disregarding if it's referenced in the scene or not
Actual: Sprite is not being loaded if it's referenced somewhere in the scene

Reproduced in: 2017.2.3f1, 2017.4.3f1, 2018.1.2f1, 2018.2.0b5

Note: when removing any Sprite references, Atlas needs to be packed two times (enter Play mode two times) for the Sprite to appear in the scene again