$str="test content %list:UnsubscriptionLink% some other %list:subscriptionLink% test";

$str="test content # some other # test";

$str="test content %list:UnsubscriptionLink% some other test";
echo preg_replace('~(%.*%)~','#',$str); //Its working

$str="test content %list:UnsubscriptionLink% some other %list:UnsubscriptionLink% test";
echo preg_replace('~(%.*%)~','#',$str); //Its Not working

<?php
$str="test content %list:UnsubscriptionLink% some other %list:UnsubscriptionLink% test";
echo preg_replace('~(%[^%]+%)~','#',$str);

test content # some other # test

~%[^%]+%~

<?php
    $str="test content %list:UnsubscriptionLink% some other %list:UnsubscriptionLink% test";
    echo preg_replace('~%[^%]+%~','#',$str);
?>

test content # some other # test