You are correct, a hash could be used to track number of occurrances of a given line in a file. I construct my hash from an initial array of all the lines you'd like to be present in the file and go from there.

use strict;

# more lines could be added to this list
my @lines = ("set CMP_DATA_INBND_DIR=C:\\h\\csscs\\data\\commi\\tmp_qu
+eue",
             "set CMP_DATA_OUTBND_DIR=C:\\h\\CMP\\data\\outbound",
             "set JAVA_HOME=C:\\h\\COTS\\JAVA2\\1.3",
             "set CSSCS_DATA=C:\\h\\csscs\\data");

# construct a hash of initial line count 
# e.g.
# (
#   lineA => 0,
#   lineB => 0
#   ...
# )
my %lines = map { $_ => 0 } @lines;

my $file = shift
  or die "Input file argument missing!\n";
my $outfile = shift;
# determine default output file name if not specified by the user.
$outfile ||= "$file.out"; 

open (IN, "<$file")
  or die "Failed to open file $file!\n";
open (OUT, ">$outfile")
  or die "Failed to open file $outfile!\n";

while (<IN>) {
  chomp;
  # increment line count if present in the file
  $lines{$_}++ if exists $lines{$_};
  # for now just print back to the output file
  print OUT "$_\n";
}

for (keys %lines) {
  # print lines that were missed from the input file
  # (count 0)
  print OUT $_ . "\n" unless $lines{$_};
}

close(IN);
close(OUT);
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Sample input file:

set FOO=BAR
set CMP_DATA_INBND_DIR=C:\h\csscs\data\commi\tmp_queue
set BAR=FOO
set CSSCS_DATA=C:\h\csscs\data
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And output file generated by the script:

set FOO=BAR
set CMP_DATA_INBND_DIR=C:\h\csscs\data\commi\tmp_queue
set BAR=FOO
set CSSCS_DATA=C:\h\csscs\data
set CMP_DATA_OUTBND_DIR=C:\h\CMP\data\outbound
set JAVA_HOME=C:\h\COTS\JAVA2\1.3
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update: added some badly needed comments..

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# Under Construction
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