Drupal Commerce - Update profile on order without cloning?
How about something like this leveraging Drupal's Entity API:

//assume we retrieved the $order_id via a page callback argument or something similar
$my_order = entity_load('commerce_order', array($order_id));

$billing_profile_id = $my_order[$order_id]-&gt;commerce_customer_billing[LANGUAGE_NONE][0]['profile_id'];
$billing_profile = entity_load('commerce_customer_profile', array($billing_profile_id));

// **replace this comment with PHP logic to update the profile values**

//save our customer profile object using the updated values from logic above
$success = entity_save('commerce_customer_profile', $billing_profile[$billing_profile_id]);


This allows us to directly edit the customer profile object associated with a particular order, and leaves the rest of the profiles unaffected.