Did you already made some changes to the theme’s files before you made the child theme? If yes, then of course those changes wouldn’t be transferred over. You would need to redo the customisations again using the child theme.
When you switch to a child theme, only certain settings would be reset. These are the Custom Menu, Custom Header, and Custom Background. In the case of Custom Menu, you can just go to WP Admin > Appearance > Menus and reassign the custom menu again. This is just the way WordPress works. All other settings in Graphene Options should stay intact.