$whole_thing =~
      m|<some unique html start string>(.*?)<end string>|s;
    $good_chunk = $1;
[download]

The matching could fail here, so you should check before using $1, otherwise you'll get the value remaining from the previous positive evaluation. You could also evaluate in list context:

($good_chunk) = $whole_thing =~
      m|<some unique html start string>(.*?)<end string>|s;
[download]

even if readability could suffer a bit here. This will assign $1 to $good_chunk if the regex matches, undef otherwise.