#!/usr/bin/perl
use strict;
use warnings;

my $text = <<EOT;
<p>This is a line
with a break.</p><pre>This is a pre
with a break.</pre><p>This is a line
with a break.</p>
EOT

1 while $text =~ s{^((?:(?!<pre>).|<pre>(?:(?!</pre>).)*</pre>)*?)\n}{$1<br/>}is;
print $text;