I tried the following :

#! /usr/bin/perl -w

use strict;
use warnings;

my $data;
{
  local($/) = undef;
  $data = <DATA>;
  $data =~ s/\n\|\|/\|\|/sg;
  print "$data";
}

__DATA__
some stuff
more
embedded crlf
||and other stuff
end
[download]

produces:

some stuff
more
embedded crlf||and other stuff
end
[download]

inman