unlink() does not clear the cache if you are performing file_exists() on a remote file like:
<?php
if (file_exists("ftp://ftp.example.com/somefile"))
?>

In this case, even after you unlink() successfully, you must call clearstatcache().
<?php
unlink("ftp://ftp.example.com/somefile");
clearstatcache();
?>

file_exists() then properly returns false.