Repro steps:

1. Open attached project (Using 5.4.x - 5.5.x)
2. Look at the gradient values on the "Cube" prefab in the "Project" window
3. Look at the gradient values on the "Cube" in the "Hierarchy" window
4. Open the same project (Using 5.6.x and above)
5. Look at the gradient values on the "Cube" prefab in the "Project" window (Everything is the same as before, as expected)
6. Look at the gradient values on the "Cube" in the "Hierarchy" window (The Gradient changed to the prefabs gradient, not expected)

Expected result: For both of the gradients to stay the same as set before
Actual result: The prefabs gradient stayed the same,while the objects gradient changed back to the prefabs gradient.

Reproduced with: 5.6.0f3 ,5.6.0p1 ,5.6.0p2 ,2017.1.0a6 ,2017.1.0b1 ,2017.1.0b2
Regression introduced in: 5.5.3p2

Note:
After completing the steps and seeing the change in the gradients values, if you open the project again with 5.4.x - 5.5.x, the gradient changes back to what it was set (Different than the prefab)
Also attached gifs