Like this?

#! perl -slw
use strict;

my( $first, $nFirst, $last, $nLast );
while( <DATA> ) {
    if( /##Flag##/ ) {
        ( $first ) = <DATA> =~ m[T:\s*(\d+)];
        $nFirst = $.;
    }
    elsif( /##CloseFlag##/ ) {
        printf "%d lines diff: %d\n", $nLast - $nFirst +1, $last - $fi
+rst;
    }
    ( $last ) = m[T:\s*(\d+)];
    $nLast = $.;
}

=output
c:\test>junk70
3 lines diff: -80508
4 lines diff: -556
=cut

__DATA__
##Flag##
some T:89898
data T:3434
here T: 9390
##CloseFlag##
some data
##Flag##
some T:898
data T:34
here T: 990
again T:342
##CloseFlag##
[download]