How to customize default Unity preferences

I am not sure if I can approach this issue somehow else. The problem is that when Unity crashes my custom settings in Unity’s preferences revert to default. I would like to keep, for example, the custom interface color setting for run mode, even after Unity has crashed, without having to reset it manually. Is there an easy way to do so?

Have you been able to save your project and all of your files after making the changes and before the crash? I know some things like the screen layout are saved in the project settings, so when you load the project, the UI reverts back to the settings for that project.

Maybe save your project/scene before the crash if you can. I have not tried this, but I know it can be an issue with the layout settings.