To reproduce:
1.Create new project.
2.Check quality settings.
3.Play any scene in project.
4.Close Unity Editor.
5.Open project again and check quality settings.
6.Notice that default per-platform settings located in "ProjectSettings/QualitySettings.asset" got erased.

Additional information:
It seems like Application::ExitPlayMode() is never called when we close Unity editor, that is why quality per-platform settings gets lost in this way.