Drupal Commerce Line Item temporary delete?
Turned out the issue was simpler than I thought.  If you think about the field between line_items and orders as a reference, it makes sense to just remove that reference, save the order, than re-add it later.  I assume the issue was arising that Drupal didn't like deleting than recreating the exact same line_item, so if it isn't ever deleted, than the reference can just be updated.