i have taken file 2 in hash_cua and file1 in hash_vppcl 
foreach my $h_esid (keys(%hash_cuat)) 
{ 
   #print "$h_esid\n"; 
   foreach my $h_etid (keys %{$hash_cuat{$h_esid}}) 
   { 
        #print "$h_etid\n"; 
        if (not exists ($hashc_cvppcl{$h_esid}{$h_etid})) 
        { 
           $res = `grep $h_esid $cuat_txns | grep $h_etid >> FOUND_UAT_MISSING_PROD.txt`; 
           next; 
        } 
        foreach my $h_cust_id (keys %{$hash_cuat{$h_esid}{$h_etid}}) 
        { 
            #for variance in cust id adding it to variance hash as "custid_var" = 'Y' and moving to next element in the loop 
            if(not exists  ($hash_vppcl{$h_esid}{$h_etid}{$h_cust_id}) ) 
                { 
                        $variance_hash{$h_esid}{$h_etid}{'cust_id_var'} = 'Y'; next; 
                } 
            foreach my $h_amount (keys %{$hash_cuat{$h_esid}{$h_etid}{$h_cust_id}}) 
                { 
                if(not exists  ($hash_vppcl{$h_esid}{$h_etid}{$h_cust_id}{$h_amount})) 
                { 
                    $variance_hash{$h_esid}{$h_etid}{'prod_amount'} = $h_amount; 
                    $variance_hash{$h_esid}{$h_etid}{'cuat_amount'} =  (keys %{$hash_vppcl{$h_esid}{$h_etid}{$h_cust_id}})[0]; #### 
                    next; 
                } 
                foreach my $h_date (keys %{$hash_cuat{$h_esid}{$h_etid}{$h_cust_id}{$h_amount}}) 
                { 
                             if(exists ($hash_vppcl{$h_esid}{$h_etid}{$h_cust_id}{$h_amount}{$h_date})) 
                             { 
                                print PRESENT "$h_cust_id|$h_date|$h_etid|$h_esid|$h_amount\n"; 
                             } 
                             else 
                             { 
                                 $variance_hash{$h_esid}{$h_etid}{'entry_date_var'} = 'Y'; 
                             } 
                } 
            } 
        } 
   } 
}

my %hash; 
while (my $line = <$FILE1>) { 
     chomp $line; 
     my  $key = (split /\|/, $line, 2)[0]; 
     $hash{$key} = $line; 
}

while (my $line2 = <$FILE2>) { 
     chomp $line2; 
     my  $key = (split /\|/, $line2, 2)[0]; 
     print "missing line: $line \n" and next unless defined $hash{$key}; 
     next if $line2 eq $hash{$key}; 
     # if we get here, the lines are different let's compare the fields 
     my @array1 = split /\|/, $hash{$key}; 
     my @array2 =  split /\|/, $line2; 
     for my $i (0..$#array1) { 
         print "something" if $array1[$i] ne $array2[$i] 
     }     
}

     for my $i (0..$#array1) {  
         print "something" if $array1[$i] ne $array2[$i]  
     }

my @errors; 
     for my $i (0..$#array1) {  
          push @errors, $i if $array1[$i] ne $array2[$i] ; 
     } 
print "There are some differences on fields # @errors \n";

my  $key = (split /\|/, $line)[0] ;

my  $key = (split /\|/, $line, 2)[0] ;

while (my $line2 = <$FILE2>) {  
     chomp $line2;  
     my  $key = (split /\|/, $line2, 2)[0];  
     print "missing line: $line2 \n" and next unless defined $hash{$key};  
     next if $line2 eq $hash{$key};  
     # if we get here, the lines are different let's compare the fields  
     my @array1 = split /\|/, $hash{$key};  
     my @array2 =  split /\|/, $line2;  
     my @errors;  
     for my $i (0..$#array1) {   
          push @errors, $i if $array1[$i] ne $array2[$i] ;  
     }  
     print "There are differences on fields # @errors in line keyed $key\n";   
}

There are differences on fields # 2 3 5 in line keyed 12345678

     print "There are differences on fields # @errors in line  $line2\n";

     print "There are differences in line  $line2 on fields @array2[@fields] \n"; # could also be  @array1[@fields] if you prefer

  print "missing line: $line " and next unless defined hash{$key};

 print "missing line: $line " and next  unless exists hash{$key};

    
This checks for the wohle line ..is nt it ? 
 next if $line2 eq $hash{$key};

next if $line2 eq $hash{$key};

my %hash;  
while (my $line = <$FILE1>) {  
     chomp $line;  
     my  $key = (split /\|/, $line, 2)[0];  
     push @{$hash{$key}}, $line;  
}

WHILE_LOOP: while (my $line2 = <$FILE2>) {  
     chomp $line2;  
     my  $key = (split /\|/, $line2, 2)[0];  
     print "missing line: $line \n" and next unless defined $hash{$key};  
     for my $i (0..scalar @{$hash{$key}) { 
          if ( ${$hash{$key}->[$i]}) eq $line2) { 
               delete ${$hash{$key}->[$i]}; 
               next WHILE_LOOP; 
          } 
    } 
    # if we get here, no line was found to be identical but be do not know which one to compare field by field. 
     # Can we just pick any?  
     my $line1 = shift @{$hash{$key}; 
     my @array1 = split /\|/, $line1;  
     my @array2 =  split /\|/, $line2;  
     for my $i (0..$#array1) {  
         print "something" if $array1[$i] ne $array2[$i]  
     }      
}

 push @{$hash{$key}}, $line;

 for my $i (0..scalar @{$hash{$key}) {  
          if ( ${$hash{$key}->[$i]}) eq $line2) {  //What are we searching. 
               delete ${$hash{$key}->[$i]};  
               next WHILE_LOOP;  
          }

push @{$hash{$key}}, $line;

use Data::Dumper;

print Dumper \%hash:

 for my $i (0..scalar @{$hash{$key}) {   
          if ( ${$hash{$key}->[$i]}) eq $line2) {  //What are we searching.  
               delete ${$hash{$key}->[$i]};   
               next WHILE_LOOP;   
          }

WHILE_LOOP: while (my $line2 = <$FILE2>) {   
     chomp $line2;   
     my  $key = (split /\|/, $line2, 2)[0];   
     print "missing line: $line \n" and next unless defined $hash{$key};   
     for my $i (0..scalar @{$hash{$key}) {  
          if ( $hash{$key}[$i]) eq $line2) {  
               delete $hash{$key}[$i]};  
               next WHILE_LOOP;  
          }  
    }  
    # if we get here, no line was found to be identical but we do not know which one to compare field by field.  
     # Can we just pick any?   
     my $line1 = shift @{$hash{$key}};  
     my @array1 = split /\|/, $line1;   
     my @array2 =  split /\|/, $line2;   
     for my $i (0..$#array1) {   
         print "something" if $array1[$i] ne $array2[$i]   
     }       
}