This repros easily in our project:
- In DefaultEngine.ini, under [/Script/Engine.RendererSettings], add: r.SceneRenderTargetResizeMethod=2
- Open the Editor, in Project Settings, User Interface, change Render Focus Rule
- Take a look at DefaultEngine.ini, it has moved the entire [/Script/Engine.RendererSettings] section to the bottom of the file, and your custom r.SceneRenderTargetResizeMethod=2 setting is gone.
Looks like a bug?