Roger, sounds like the situation is unclear.
My assumption was that the Drupal root and the domain root were the same, in your case public_html. It sounds like that is not the case. Drush would not have gone outside the Drupal root to delete a php.ini file. So I think my theory as to your problem is probably wrong.
FYI, since my early days of using Drupal I standarized on always making the Drupal root and the domain root the same. In theory, Drupal doesn't require that, but I have just been plagued by problems whenever I try otherwise. I'm not saying that is your problem here, just sharing my (bad) experiences with implementing Drupal outside the domain root.