<?php

$removePath = '/path/to/exist-not' ;
$includepath = '.' . PATH_SEPARATOR . '/path/to/exist-not' . PATH_SEPARATOR . '/path/to/exist';
$wordsPath = str_replace(PATH_SEPARATOR, ' ', $includepath);
$result = preg_replace('/\b' . preg_quote($removePath, '/') . '\b/i', '', $wordsPath);
var_dump(str_replace(' ', PATH_SEPARATOR, $result));

$paths = array_flip(explode(PATH_SEPARATOR, $includepath));
if(isset($paths[$removePath])){
	unset($paths[$removePath]);
}
$includepath = implode(PATH_SEPARATOR, array_flip($paths));
var_dump($includepath);