You'd endear yourself more if you followed the (simple) local formatting conventions.

Lots of room for error checking, but ought to work. (Note: This writes the file directly. No redirection required.)

#! perl -slw
use strict;
use constant batchdir => "e:\meta";
use constant {
    infile  => batchdir . "\DDNs3";
    nfile2  => batchdir . "\DDNsUid2";
    outfile => "DDNs3.ldif",  ## Assume outfile n current dir per .cmd
};

unlink outfile; ## If there delete it; silently do nothing if not.

open DN,  '<', infile  or die $!;
open UID, '<', infile2 or die $!;
open OUT, '>', outfile or die $!;

while( <DN> ) {
    chomp;
    print OUT "dn: $_";
    print OUT "changetype: notify";
    print OUT "replace: employeeNumber";

    chomp( my $empNo = <UID> );
    print OUT "employeeNumber: $empNo";
}
close OUT;
close UID,
close DN;


__END__
@echo on

::Set BATCH Input Directory
set batchdir=e:\meta

::Set the input file containing the list
set infile=%batchdir%\DDNs3
set infile2=%batchdir%\DDNsUid2

::If exists, we remove output file
rm DDNs3.ldif

::For loop below process each line in the input list.

:uid
FOR /F "tokens=* delims=" %%i IN (%infile%) do (
echo dn: %%i
echo changetype: modify
echo replace: employeeNumber
call :loop2
)
goto :eof
:loop2
FOR /F "tokens=* delims=" %%k IN (%infile2%) do (
echo employeeNumber: %%k
echo.
call :uid
)

:eof
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