my $lines = join "", <DATA>;
$lines =~ s/\n\n=/=/gm;
print $lines;
__DATA__
line 1

======
line after break line

##</code><code>##

line 1======
line after break line

##</code><code>##

line 1
======
line after break line

##</code><code>##

$/ = '=';
while (<DATA>) {
    s/\n\n=/\n=/m;
    print;
}
__DATA__
line 1

======
line after break line

##</code><code>##

line 1
======
line after break line