use strict;
use warnings;
my @refnos = ();

my $old = <<OLD;
UTRIR8709990166
ZPHLHLKJ87
OLD

my %oldPayments;

open my $payments, '<', \$old;
%oldPayments = map {$_ => undef} grep {chomp; length} <$payments>;
close $payments;

print "Reading UTR Payment numbers \n";

while (<DATA>) {
    chomp;
    my @data = split (/~/, $_);
    (my $utr = uc $data[1]) =~ s/\s*//g;

    next if exists $oldPayments{$utr};
    $oldPayments{$utr} = $data[1];
    print "Payment $utr received of $data[2]\n";
}

open $payments, '>', \$old;
print $payments join "\n", sort keys %oldPayments, '';
close $payments;

print "New payments are:\n   ";
print join "\n   ", grep {defined $oldPayments{$_}} sort keys %oldPayments;

__DATA__
0906928472847292INR~UTRIR8709990166~     700000~INR~20080623~RC425484~IFSCSEND001                       ~Remiter Details ~1000007   ~TEST RTGS TRF7                     ~                                   ~                                   ~ ~RTGS~REVOSN OIL CORPORATION   ~IOCL  ~09065010889~0906501088900122INR~         7~         1~ 1
0906472983472834HJR~UTRIN9080980866~    1222706~INR~20080623~NI209960~AMEX0888888                       ~FRAGNOS EXPRESS - TRS CARD S DIVISI~4578962   ~/BNF/9822644928                    ~                                   ~                                   ~ ~NEFT~REVOSN OIL CORPORATION   ~IO    CL  ~09065010889~0906501088900122INR~         7~         1~ 1
0906568946748922INR~ZP HLHLKJ87 ~ 1437865.95~INR~20080623~NI209969~HSBC0560002                       ~MOTOSPECT UNILEVER LIMITED ~1234567   ~/INFO/ATTN:                        ~//REF 1104210 PLEASE FIND THE DET  ~                                   ~ ~NEFT~REVOSN OIL CORPORATION   ~IOCL  ~09065010889~0906501088900122INR~         7~         1~ 1
0906506749056822INR~Q08709798905745~    5960.74~INR~20080623~NI209987~                                  ~SDV AIR LINK REVOS LIMITED ~458ss453  ~                                   ~                                   ~                                   ~ ~NEFT~REVOSN OIL CORPORATION   ~IOCL  ~09065010889~0906501088900122INR~         7~         1~ 1
0906503389054302INR~UTRI790898U0166~       2414~INR~20080623~NI209976~                                  ~FRAGNOS EXPRESS - TRS CARD S DIVISI~          ~/BNF/9826805798                    ~                                   ~                                   ~ ~NEFT~REVOSN OIL CORPORATION   ~IOCL  ~09065010889~0906501088900122INR~         7~         1~ 1

##</code><code>##

Reading UTR Payment numbers 
Payment UTRIN9080980866 received of     1222706
Payment Q08709798905745 received of     5960.74
Payment UTRI790898U0166 received of        2414
New payments are:
   Q08709798905745
   UTRI790898U0166
   UTRIN9080980866