You could read the entire file in with file_get_contents(), perform a str_replace(), and output it back with file_put_contents().
Sample code:
<?php
$path_to_file="path/to/the/file";
$file_contents = file_get_contents($path_to_file);
$file_contents = str_replace("\nH", ",H", $file_contents);
file_put_contents($path_to_file, $file_contents);
?>