Rules: How to modify an existing condition programmatically
So turned out it was quite easy:

  $hk_delivery_rule = rules_config_load('commerce_shipping_service_hong_kong_delivery');

  foreach ($hk_delivery_rule-&gt;conditions() as $condition) {

    if (isset($condition-&gt;settings['second_price'])) {

      $condition-&gt;settings['second_price']['amount'] = $hk_threshold;

    }

  }

  $hk_delivery_rule-&gt;save();