Assuming you are only concerned with repeated numbers in consecutive lines, then something like this would do (untested):

use strict;     #### Always have these lines.  
use warnings;   #### They will save you lots of time debugging

use DBI;
use Time::localtime;
use File::Compare;

use XML::Simple; # qw(:strict);
use Data::Dumper;

my $user = "213256";

my @filesToProcess = glob "/export/home/$user/Tests/Match/dummy2*";   
+ #### Need ""s.  ''s do not do variable interpolation

foreach my $file (@filesToProcess)
{
  open(FILE, $file) or die "Can't open `$file': $!";

  my $prev_var = -1_000_000;         #### set this to a value that wil
+l never appear as the numbers you need to check.
                                     #### (Obviously the 2-digit numbe
+rs must be in the range 0 to 99)

  while ( my $line = <FILE> )        #### do NOT read entire files int
+o memory if they are big.  Much better to process them a line at a ti
+me
  {
    chomp $line;

    my $var = substr($line, 10, 2);  #### Do you mean substr($line,   
+ 9   , 2)?  substr() consders the first character to be at offset zer
+o
        
    if ($var != $prev_var)           #### if number is different to nu
+mber in previous line, then process it
    {
       $prev_var = $var;

       ... process $line here ....
    }
  }

  close FILE;
}
[download]

======

Thought #1:

In your example the lines are sorted by the 2-digit number. If that is typical, then at the most you're only going to have to process 100 lines from the huge files.

Is that what you expect?

======

Thought #2:

Q: What are you supposed to do if you get repeated numbers, but in non-consecutive lines like below?

AB000000026JHAHKDFK
AB00000003033AFSFAS  = "30" line
AB000000028JHKHKHKJ
AB000000030HJHKH80J  = "30" line
AB0000000324446KJHK
AB000000030LOIKJUJ8  = "30" line
[download]

UPDATE:

Replaced:
foreach my $line ( <FILE> )        #### do NOT read entire files into memory if they are big.  Much better to process them a line at a time
with
while ( my $line = <FILE> )        #### do NOT read entire files into memory if they are big.  Much better to process them a line at a time

Embarassing bug that! In my defence the original code had 'foreach' and I probably just missed it.
Had I written the code from scratch I would (I hope!) have used 'while'. I'm still an idiot though! :)

Thanks very much to Not_a_Number for pointing this out!