Your method is fine, you're just doing something extra that you shouldn't be doing. You're ONLY printing the line to the file if it doesn't exist in your %lines hash yet. But then you're printing a newline regardless of that! Either do:

while (<DUPLICATE>) {
  print DUPremoved if not $lines{$_}++;
}
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or, if you're really adamant about chomp()ing the line first, do:

while (<DUPLICATE>) {
  chomp;
  print DUPremoved "$_\n" if not $lines{$_}++;
}
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