The problem in your is with extracting the sub parms from  @_. With

  my $file_name = ${shift()};
  my $lines_in  = ${shift()};
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you are copying your dereferenced references into new local variables, which does not update the variables in the caller. Try instead

sub read_template {

  my $file_name = shift;
  my $lines_in  = shift;
  my $line_cnt  = 0;

  if (!open (INPUT, "< $$file_name")) {
    die "Can't open $file_name as input.";
  } else {
    while (<INPUT>) {
      $line_cnt++;
      $$lines_in .= $_;
    }
    close (INPUT);
  }
  return($line_cnt);
}
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This approach keeps the references and updates the caller's variables.

-Mark