<?php
   
if (!file_exists('./'. $file->filepath)) {
     
// Missing file.
     
$errors[] = $file->filepath;
      continue;
    }
?>

Those lines assume files are located relative to drupal site dir. My files are in /some_private_location/here/.

I patched the above like so:

<?php
   
if (!file_exists($file->filepath)) {
      if (!
file_exists('./'. $file->filepath)) {
       
// Missing file.
       
$errors[] = $file->filepath;
        continue;
      }
    }
?>

But now 'file_move()' fails. It seems that drupal 6 doesn't really support private files where the file directory is outside the drupal root.
The description here confirms that http://api.drupal.org/api/drupal/includes%21file.inc/function/file_creat...
file_create_path is used to help make a drupal ONLY path... :(

Any ideas how we can fix this? Avoid using drupal PHP functions and use PHP core functions instead?