What are you using to parse the source at present? Are you looking for a chunk of code using regexen and loops, or something you can plug into a Parse::RecDescent rule set?

The following sketch code for handling the problem using regexen may help:

use strict;
use warnings;

while (<DATA>) {
    s/\[\[(\w+)/parseHereDoc ("$1")/e if /\[\[\w+/;
    print;
}


sub parseHereDoc {
    my $id = shift;
    my $str = '"';
    
    while (<DATA>) {
        last if /^$id$/;
        $str .= $_;
    }
    
    return $str . '"';
}

__DATA__
var = [[END . "other stuff";
heredoc
data
END
[download]

Prints:

var = "heredoc
data
" . "other stuff";
[download]