WordPress and SQL – Update and Insert from another table if column value doesn’t exist

Use PHP and the WordPress API. Place the following in copy-options.php and FTP it to wp-content/plugins, then activate it from the main site:

<?php

/**
 * Plugin Name: Copy Options
 * Plugin URI:  http://wordpress.stackexchange.com/q/186092/1685
 * Description: Copy options from site 2 to site 1.
 * Version:     0.1
 * Author:      TheDeadMedic
 * Author URI:  http://wordpress.stackexchange.com/users/1685/thedeadmedic
 */

function wpse_186092_copy_options() {
    if ( 2 !== $blog_id = get_current_blog_id() )
        switch_to_blog( 2 );

    // Get all options from blog 2
    $options = wp_load_alloptions();

    // Switch to main blog
    switch_to_blog( 1 );

    foreach ( $options as $name => $value )
        update_option( $name, $value ); // Will update option if exists, insert if not

    // Switch back to current blog
    switch_to_blog( $blog_id );     
}

register_activation_hook( __file__, 'wpse_186092_copy_options' );

Backup first. This code is not tested and comes without warranty.