How to reproduce:
1. Create a new Unity project
2. Import Polybrush Tool to a Unity
3. Create Plane in the Scene
4. Drag Created Plane to a Project window
5. Open Tools --> Polybrush --> Polybrush Window
6. Make some changes to a Plane with Polybrush
7. Press "Apply" in the Inspector window
8. Deselect Plane or remove it from Scene
9. Drag Plane prefab to a Scene

Expected result: Polybrush changes are saved in the Plane prefab.
Actual result: Polybrush changes are not saved in the Plane prefab.

Reproduced with: 2018.3.0a9, 2018.2.5f1, 2018.1.9f2, 2017.4.9f1, 2017.2.3p3.