Try moving the "new LDIF" to outside of the loop:

my $ldif_OUT = Net::LDAP::LDIF->new( "buildAD.ldif", "a", wrap=>40 );
while (<PERSON>){
    chomp;
    $dn = $ldap->search( #return only the employeeID DN
            base => "$BASEDN",
            filter => "(&(objectClass=user)(employeeID=$_))",
            scope => "sub",
            attrs => ['1.1']
            );
        next unless $dn; # Make sure something is returned..
    while( my $entry = $dn->pop_entry() )
    {
      $ldif_OUT->write_entry($entry);
    }
    print OUT "changetype: modify";
    print OUT "replace: manager";
    print OUT "manager: dn","\n";
}
$dn = $ldap->unbind;  #session ends
[download]

Humbled, I return for wisdom. The while statements are erratic, my wish is to have a 1to1 relationship between the while statements and the input files, yet the 2nd while <MGR> will pull results for 50 lines before the first while <PERSON> runs again. I wish to read iteratively <PERSON> one line at a time, then print @lines, then read iteratively <MGR>, one line at a time, resulting in a four lines written to OUT or buildAD.ldif.

Also, perl throws an error on the second $_ use; how else may it be defined as I wish to place the next line from <MGR> file into the filter?

Error reads: Use of uninitialized value $_ in pattern match (m//) at build4.pl line 48, <MGR> line 120 (#1)(W uninitialized) An undefined value was used as if it were already defined. It was interpreted as a "" or a 0, but maybe it was a mistake. To suppress this warning assign a defined value to your variables.

I am also puzzled why print OUT (@lines) does not print the contents of LDIFA after each line of <PERSON> is processed (instead it is printing erratically to OUT). And, why OUT fails in Net::LDAP::LDIF->new( "OUT", "a", wrap=>40 );, I am forced to hardcode "buildAD.ldif" instead of OUT.

my $ldap = Net::LDAP->new("$HOST", port=>389) or die "$@";
my $dn = $ldap->bind("$ADMIN", password=>"$PWD");
my $dnm = $ldap->bind("$ADMIN", password=>"$PWD");
my @attr = "1.1";
my $result = Net::LDAP::LDIF->new( "buildAD.ldif", "a", wrap=>40 );
my @lines = (<LDIFA>);

while (<PERSON>)
{
chomp;
$dn = $ldap->search( #return only the employeeID DN
        base => "$BASEDN",
        filter => "(&(objectClass=user)(employeeID=$_))",
        scope => "sub",
        attrs => [@attr]
        );

        next unless $dn; # Make sure something is returned
while( my $entry = $dn->pop_entry() )
{
        $result->write_entry($entry);
        if ( $result != /dn:/ )
{
        print OUT (@lines);
}
while (<MGR>)
{
chomp;
$dnm = $ldap->search( #return only the manager DN
        base => "$BASEDN",
        filter => "(&(objectClass=user)(employeeID=$_))",
        scope => "sub",
        attrs => [@attr]
        );

        next unless $dnm; # Make sure something is returned
while( my $entry = $dnm->pop_entry() )
{
        $result->write_entry($entry);
}
}
}
}

$dn = $ldap->unbind;  #session ends
$dnm = $ldap->unbind;  #session ends

close OUT2 or die "Cannot close in-memory file: $!";
close OUT or die "Cannot close in-memory file: $!";
close MGR or die "Cannot close in-memory file: $!";
close PERSON or die "Cannot close in-memory file: $!";
close LDIFA or die "Cannot close in-memory file: $!";
[download]

If you find yourself having problems with nested loops, it helps to indent your code so the structure becomes clearer:

while (<PERSON>)
{
chomp;
$dn = $ldap->search( #return only the employeeID DN
        base => "$BASEDN",
        filter => "(&(objectClass=user)(employeeID=$_))",
        scope => "sub",
        attrs => [@attr]
        );

        next unless $dn; # Make sure something is returned
while( my $entry = $dn->pop_entry() )
{
        $result->write_entry($entry);
        if ( $result != /dn:/ )
{
        print OUT (@lines);
}
while (<MGR>)
{
...
[download]

could be reindented as

while (<PERSON>)
{
    chomp;
    $dn = $ldap->search( #return only the employeeID DN
        base => "$BASEDN",
        filter => "(&(objectClass=user)(employeeID=$_))",
        scope => "sub",
        attrs => [@attr]
        );

        next unless $dn; # Make sure something is returned
    while( my $entry = $dn->pop_entry() )
    {
        $result->write_entry($entry);
        if ( $result != /dn:/ )
    {
        print OUT (@lines);
    }
    while (<MGR>)
    {
    ...
[download]

So, you'll see that once you've read to the end of MGR, you'll still have lines in PERSON. Maybe you want to look up data from the contents of MGR? Then a hash is a better structure:

my %manager;
while (<MGR>) {
    $manager{ $_ } = $ldap->search(...); # return only the manager DN
};

while (<PERSON>) {
    ... # you never seem to use the information from MGR here...
};
[download]

In addition to Corion's wise words,

Your code:

 if ( $result != /dn:/ )
[download]

probably does not do what you think it does - and I'm curious to know what you think it does.
That is probably why you are puzzled about the contents out OUT.

You probably want to see if $entry contains "dn" and negate that:

if ( $entry !~ /dn:/ )
[download]

     Syntactic sugar causes cancer of the semicolon.        --Alan Perlis

Grateful. I return with no good news. $result continues to clobber FILE, or possible print OUT clobbers FILE; either way, the desired output in an iterative format is not resolved. We pray for continued wisdom.

I have reverted to the previous code, as I am getting no where with this exploration. This code gives me the DN from ou3 file to the OUT file, but once I hit the $entry = $dn->pop_entry(): line, it breaks again. If I do not use the pop_entry() method, each result sends the following to OUT (Net::LDAP::Search=HASH(0x1c72f1c)). Is there any other way around this problem? Thanks again.

#! perl
use strict;
use warnings;
use diagnostics;

use Net::LDAP;
use Net::LDAP::Entry;
use Net::LDAP::Search;
use Net::LDAP::LDIF;

open PERSON, "<", "ou3" or die "Cannot open 'ou3': $!";
open MGR, "<", "ou8" or die "Cannot open 'ou8': $!";
open OUT, ">", "buildAD.ldif" or die "Cannot open 'buildAD.ldif': $!";

my $HOST = "11";
my $ADMIN = "cn=d";
my $PWD = "0";
my $BASEDN = "DC=corp";

my $ldap = Net::LDAP->new("$HOST", port=>389) or die "$@";
my $dn = $ldap->bind("$ADMIN", password=>"$PWD");
my @attr = "1.1";
my $result = Net::LDAP::LDIF->new( "buildAD.ldif", "a", wrap=>40 );
my $entry = <>;

while (<PERSON>){
chomp;
$dn = $ldap->search( #return only the employeeID DN
        base => "$BASEDN",
        filter => "(&(objectClass=user)(employeeID=$_))",
        scope => "sub",
        attrs => [@attr],
        );
        next unless $dn; #make sure something is returned

        $entry = $dn->pop_entry();
        $result->write_entry($entry);
        print OUT "changetype: modify";
        print OUT "replace: manager";
}

$dn = $ldap->unbind;  #session ends

close OUT or die "Cannot close in-memory file: $!";
close MGR or die "Cannot close in-memory file: $!";
close PERSON or die "Cannot close in-memory file: $!";
[download]