can't you just write a very simple str replace to replace them with normal characters e.g.
//code from the PHP manual
$text = "bláh íóú NÓTHÍNG!";
$search = array ('ç', 'á', 'é', 'í', 'ó', 'ú', 'ã', 'õ', 'â', 'ê', 'î', 'ô', 'û');
$replace = array ('c', 'a', 'e', 'i', 'o', 'u', 'a', 'o', 'a', 'e', 'i', 'o', 'u');
$export = str_replace($search, $replace, strtolower($text));
it would mean renaming all your files but it's alot easier in you cant use iconv or whatever extension deals with this crap