$re = '/(<!(--(?:[^-]|-(?!->))*?--)>)(?!((?!<%--)[\s\S])*?--%>)/';
$str = 'Condition: 1 : <!-- normal HTML comment -->
Codition: 2 <%-- normal JSP comment
<!-- inside html comment here -->
other comment stuff
<!-- another inside html comment here -->
--%>
Condition: 1 : <!-- normal HTML comment -->
';
$subst = "<%$2%>";
$result = preg_replace($re, $subst, $str);
echo "The result of the substitution is ".$result;
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php