Simple Drupal 7 script that removes aliases with empty source.

remove-drupal-aliases-with-empty-source.php

// Use this simple script in empty aliases sitaution, when you have many rows
// in "url_alias" table with "source" column being empty.

$query = db_select('url_alias', 'ua')->fields('ua');
$query->condition('ua.source', '', '=');
//$query->range(0, 500); // uncomment if plan to do this job in smaller chunks
$paths = $query->execute()->fetchAll();
foreach($paths as $object) {
    if (is_numeric($object->pid)) {
      path_delete($object->pid);
    }
}