Exclude 2 in 3 terms of A Taxonomy from all Archives

Few remarks:

• I use pre_get_posts as an action hook, not as a filter.
• You should use ! is_admin() to prevent this from changing your backend views.
• You should skip the 'relation' => 'OR', since you only have a single tax_query filter
• Is there any reason why you have to modify the post type ? Is your custom taxonomy attached to multiple post types?

so you could try this modification instead:

add_action( 'pre_get_posts', 'change_archive_loop' );

function change_archive_loop( $query ) {
    $choduyet = intval( get_option( 'zen-id_cho_duyet' ) );
    $baocao = intval( get_option( 'zen-id_bao_cao' ) );
    if ( ! is_admin() && $query->is_tax( 'tinh-trang' ) && $query->is_main_query() ) {
        $terms = array( $choduyet, $baocao );
        $query->set( 'tax_query', array(
            array(
                'taxonomy' => 'tinh-trang',
                'field' => 'id',
                'operator' => 'NOT IN',
                'terms' => $terms
            )
        ) );
    }
 }