Painted speed trees are not updated when it's prefab scaling is changed after the project is upgraded to Unity with improved prefabs

Steps to Repro:
1. Open the attached project or create a new project with Unity 2018.2 or lower version
2. Hierarchy > right click
3. 3D Object > terrain
4. Select 'paint tree' tab on terrain > edit tree > add tree
5. Add speed tree prefab > paint it on terrain
6. Now open the project with Unity 2018.3.a6 or higher version
5. Change the prefab's scale
6. go back to 'paint tree' tab and click refresh

Actual Result:
1. New prefab's scale is not reflecting on terrain
2. Artifacts are appearing in-game and scene view

Expected Result:
1. When prefab's scale is modified, it's scale on terrain should change

Environment:
Windows and Mac

Occurring with:
2018.3.0a10, 2018.3.0a6

Note:
Improved prefabs were added from 2018.3.0a6

Working with:
2018.3.0a5, 2018.3.0a1