$re = '~\[\?\](?:(?!\[/?\?\]).)*%empty%(?:(?!\[\?\]).)*\[/\?]~ms';
$str = '[?]<h1>%empty%</h1>
<p>text</p>
[/?]
text
[?]<h1>%empty%</h1>
<p>text</p>
[/?]
text
[?]<h1>%!empty%</h1>
<p>text</p>
[/?]
text
[?][][/<h1>%empty%</h1>][][[[]]]
<p>text</p>
[/?]
[?]<h1>%empty%</h1>
<p>text</p>[?]
[/?]
text[?]<h1>%!empty%</h1>
<p>text</p>
[/?] ';
$subst = "REPLACED";
$result = preg_replace($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