per le prime tre righe
codice:
<?php
$handle = fopen("file.txt", "r");
$n = 0;
while (!feof($handle) && $n < 3) {
   $buffer[] = fgets($fd, 4096);
   ++$n;
}
fclose($handle);
?>
per eliminare le doppie righe nuove invece devi fare un ciclo
codice:
$lines = file("file.txt");
$new_lines = array();
foreach($lines as $key=>$line) {
      if(trim($line) == '' && isset($lines[$key+1]) && trim($lines[$key+1]) == '') {
              continue;
      } else {
              $new_lines[] = trim($line);
      }
}

$fd = fopen("file.txt", "w");
fwrite($fd, implode('\n', $new_lines));
fclose($fd);