How do you Permanently Delete Sidebars

Thanks for the comment @Rarst! That was the issue. For whatever reason I had that extra sidebar method call in there and that was causing the problem.

register_sidebar(
    array(
        'name' => 'Sidebar'
    )
);
register_sidebar(
    array(
        'name' => 'Sub Menu'
    )
);

WordPress saves the data from the widgets in the DB but it doesn’t save the widgets themselves – that is controlled entirely by the theme.

Thanks!