Save Scene Dialog appears twice on clicking "Don't Save" on changing Graphics API

Steps to repro:
1. Create a new Project > Create Cube.
2. File > Build Settings > Player Settings.
3. Uncheck Auto Graphics API for Windows.
4. Select Direct3D12 and drag it to the top in the list.
5. Restart the editor > Click on Don't Save button.

Actual Result:
Save scene pop up appears twice

Expected Result:
Editor should restart

Reproducible in:
2020.1.0a3, 2019.3.0b2, 2019.2.0f2, 2019.1.10f1

Working fine in:
2018.3.0f2

Environment: Mac 10.14 and Windows 10

Note: Similar bug is reported earlier in different scenario https://fogbugz.unity3d.com/f/cases/1166643/
In that bug, Save Scene Dialog was not able to close on clicking the close button or cancel button