Could you provide a url and wp admin credentials so that we can actually check what is going on?
The description of the problem you are providing is frankly quite vague and it’s impossible for us to help based on such descriptions.
1) What theme are you using?
2) Only switching to a differnt theme in wordpress will reset your widgets and menus. Installing GD shouldn’t change anything in your widget areas. Unless you are using dynamic custom widget areas with some particular theme that are faulty (that’s why question n1)
3) Modifying the theme compatibility (unless you modify the code of the plugin files) create a themename_custom option so that upon update your custom work is not wiped out. In our tests, updating doesn’t remove any custom settings, are you saying that after updating all your custom settings in GD >> Theme Compatibility disappeared?
Let us know and please don’t forget a link and wp admin credentials.
Thx