To reproduce:

1.Download and open attached project.
2.Run the editor script by going to Menu -> Reproduce and press "Disable Box Colliders".
3.Notice how box collider from Cube gameObject is disabled.
4.Save and exit Unity.
5.Load up the project again.

Expected result: changes are saved and box collider component of Cube gameObject is still disabled.
Actual result: changes are not saved and box collider component is enabled.

Reproduced with: 5.6.0b8, 5.5.1p2, 5.4.4p2, 5.3.7p2

Notes : Changes aren't registered after running the editor script. if there are any additional changes made to the project, for example added another gameObject after running the editor script changes are then registered and saved.