Here's an example as a first shot at this:

#!/usr/local/bin/perl
# repl.pl
use strict;
open INPUT, "<input.txt" or die "Blerch: $!\n";
open OUTPUT, ">output.txt" or die "Hcrelb: $!\n";
my $replace_string="Hi there.\n";
my $flag=0;
my %markers=("BEGIN" => "<!- Begin Replacable Section-->",
             "END" => "<!- End Replacable Section-->",
            );
while (<INPUT>) {
  if ($flag) {
    next unless /$markers{END}/;
    $flag=0;
    print OUTPUT $replace_string;
  }
  print OUTPUT;
  $flag=1 if /$markers{BEGIN}/;
}
__END__
> cat input.txt
But now I know that twenty centuries of stony sleep
were vexed to nightmare by a rocking cradle.
And what rough beast, it's hour come round at last,
slouches towards Betlehem to be born?
<!- Begin Replacable Section-->
A poem
<!- End Replacable Section-->
W. B. Yeats

> repl.pl ; cat output.txt
But now I know that twenty centuries of stony sleep
were vexed to nightmare by a rocking cradle.
And what rough beast, it's hour come round at last,
slouches towards Betlehem to be born?
<!- Begin Replacable Section-->
Hi there.
<!- End Replacable Section-->
W. B. Yeats
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Robartes-