$re = '/(?sm)(?:^\[0\d{2}]|\G(?!\A)).*?\R\[\K\?{3}(?=.*?\R\[0)/';
$str = '[000] Foo
[???] Foo
[020] Foo
[???] Foo
[045] Foo
[???] Foo
[???] Foo
[100] Foo
[???] Foo
[???] Foo
[115] Foo
[???] Foo';
$subst = "1??";
$result = preg_replace($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