Replace non-existent files with empty file using Drupal {file} table.

gistfile1.php

// REPLACE?
$replace = FALSE;
// path to empty file
$source = 'files/empty.png';

// RUN
$result = db_query('SELECT fid, filename, filepath FROM {files}');
$src = file_create_path($source);
$src_exists = file_exists($src);
$i = 1;
while ($f = db_fetch_object($result)) {
  $dest = file_create_path($f->filepath);
  if (!file_exists($dest)) {
    $out .= $i++ . '. ' . $f->filepath . "\n";
    if ($replace && $src_exists) { 
      copy($src, $dest);
      chmod($dest, 0664);
      db_query("UPDATE {files} SET origname='%s' WHERE fid=%d", 'empty.png', $f->fid);
    }
  }
}
return $out;