Changing CPT slug and taxonomy already registered in parent theme

WordPress 4.5 introduced the functions unregister_post_type() and unregister_taxonomy(). You could deregister your post type respectively taxonomy and register them again with your custom settings. The post type is still named portfolio. You could rename it, but you would probably have to check your template files for references.

add_action('init', 'wpse_247924_overwrite_theme_post_types', 1000);
function wpse_247924_overwrite_theme_post_types() {

    unregister_post_type( 'portfolio' );

    $labels = array(
        'name' => __( 'Portfolio', 'read' ),
        'singular_name' => __( 'Portfolio Item', 'read' ),
        'add_new' => __( 'Add New', 'read' ),
        'add_new_item' => __( 'Add New', 'read' ),
        'edit_item' => __( 'Edit', 'read' ),
        'new_item' => __( 'New', 'read' ),
        'all_items' => __( 'All', 'read' ),
        'view_item' => __( 'View', 'read' ),
        'search_items' => __( 'Search', 'read' ),
        'not_found' =>  __( 'No Items found', 'read' ),
        'not_found_in_trash' => __( 'No Items found in Trash', 'read' ),
        'parent_item_colon' => '',
        'menu_name' => 'Portfolio'
    );

    $args = array(
        'labels' => $labels,
        'public' => true,
        'exclude_from_search' => false,
        'publicly_queryable' => true,
        'show_ui' => true,
        'query_var' => true,
        'show_in_nav_menus' => true,
        'capability_type' => 'post',
        'hierarchical' => false,
        'menu_position' => 5,
        'supports' => array( 'title', 'editor', 'thumbnail', 'comments', 'revisions' ),
        'rewrite' => array(
            'slug' => 'conteudo',
            'with_front' => false
        )
    );

    register_post_type( 'portfolio' , $args );

    unregister_taxonomy( 'department' );

    $labels_dep = array(
        'name' => __( 'Departments', 'read' ),
        'singular_name' => __( 'Department', 'read' ),
        'search_items' =>  __( 'Search', 'read' ),
        'all_items' => __( 'All', 'read' ),
        'parent_item' => __( 'Parent Department', 'read' ),
        'parent_item_colon' => __( 'Parent Department:', 'read' ),
        'edit_item' => __( 'Edit', 'read' ),
        'update_item' => __( 'Update', 'read' ),
        'add_new_item' => __( 'Add New', 'read' ),
        'new_item_name' => __( 'New Department Name', 'read' ),
        'menu_name' => __( 'Departments', 'read' )
    );

    register_taxonomy(
        'material',
        array( 'portfolio' ),
        array(
            'hierarchical' => true,
            'labels' => $labels_dep,
            'show_ui' => true,
            'public' => true,
            'query_var' => true,
            'rewrite' => array(
                'slug' => 'material'
            )
        )
    );


    $labels_tag = array(
        'name' => __( 'Portfolio Tags', 'read' ),
        'singular_name' => __( 'Portfolio Tag', 'read' ),
        'search_items' =>  __( 'Search', 'read' ),
        'all_items' => __( 'All', 'read' ),
        'parent_item' => __( 'Parent Portfolio Tag', 'read' ),
        'parent_item_colon' => __( 'Parent Portfolio Tag:', 'read' ),
        'edit_item' => __( 'Edit', 'read' ),
        'update_item' => __( 'Update', 'read' ),
        'add_new_item' => __( 'Add New', 'read' ),
        'new_item_name' => __( 'New Portfolio Tag Name', 'read' ),
        'menu_name' => __( 'Portfolio Tags', 'read' )
    );

    register_taxonomy(
        'portfolio_tags',
        array( 'portfolio' ),
        array(
            'hierarchical' => false,
            'labels' => $labels_tag,
            'show_ui' => true,
            'public' => true,
            'query_var' => true,
            'rewrite' => array(
                'slug' => 'portfolio_tags'
            )
        )
    );

}