I tried using the suggestions by chromatic and almut:

#!/usr/bin/perl

use strict;
use warnings;
use File::Copy "cp";

my $confINPUT;
my ($i)           = 0;
my ($date)        = &getDate;
my ($confOutName) = shift @ARGV;

die "$!\n" unless open CONF_ID,   '<',  "@ARGV";
die "$!\n" unless open CONFLIST1, '>>', 'conf_list1.tmp';
die "$!\n" unless open CONFLIST2, '>>', 'conf_list2.tmp';
die "$!\n" unless open CONFLIST3, '>>', 'conf_list3.tmp';
die "$!\n" unless open CONFADD,   '>>', "./additions/additions_$ARGV[0
+]_date";
while ( defined( $_ = <CONF_ID> ) ) {
    next unless /\S/;
    die "$!\n" unless open TEMPLATE1, '<', './templates/conf_template'
+;
    die "$!\n" unless open TEMPLATE2, '<', './templates/conf_template2
+';
    die "$!\n" unless open TEMPLATE3, '<', './templates/conf_template3
+';
    $confINPUT = $_;
    my ( $confID, $confPIN ) = split( " ", $confINPUT, 3 );
    while ( defined( $_ = <TEMPLATE1> ) ) {
        $_ =~ s/XXXXXX/$confID/g;
        print CONFLIST1 $_;
    }
    while ( defined( $_ = <TEMPLATE2> ) ) {
        $_ =~ s/XXXXXX/$confID/g;
        $_ =~ s/AAAA/$confPIN/g;
        print CONFLIST2 $_;
    }
    while ( defined( $_ = <TEMPLATE3> ) ) {
        $_ =~ s/XXXXXX/$confID/g;
        print CONFLIST3 $_;
    }
    die "$!\n" unless close TEMPLATE1;
    die "$!\n" unless close TEMPLATE2;
    die "$!\n" unless close TEMPLATE3;
}
die "$!\n" unless close CONFLIST1;
die "$!\n" unless close CONFLIST2;
die "$!\n" unless close CONFLIST3;
die "$!\n" unless open CONFLIST1, '<', 'conf_list1.tmp';
die "$!\n" unless open CONFLIST2, '<', 'conf_list2.tmp';
die "$!\n" unless open CONFLIST3, '<', 'conf_list3.tmp';
print CONFADD "; start conference config 1\n";
while ( defined( $_ = <CONFLIST1> ) ) {
    print CONFADD $_;
}
print CONFADD "\n\n; start conference config 2\n";
while ( defined( $_ = <CONFLIST2> ) ) {
    print CONFADD $_;
}
print CONFADD "\n\n; meetme_additional_custom.conf\n";
while ( defined( $_ = <CONFLIST3> ) ) {
    print CONFADD $_;
}
close CONFADD;
die "$!\n" unless close CONFLIST1;
die "$!\n" unless close CONFLIST2;
die "$!\n" unless close CONFLIST3;
cp( "$ARGV[0]", "./finished_list/@ARGV.finished" );
unlink "$ARGV[0]";
die "$!\n" unless unlink 'conf_list1.tmp';
die "$!\n" unless unlink 'conf_list2.tmp';
die "$!\n" unless unlink 'conf_list3.tmp';
print "Number of Entries processed: $i\n";
exit 0;

sub getDate() {
    my (@months)   = qw(Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov De
+c);
    my (@weekDays) = qw(Sun Mon Tue Wed Thu Fri Sat Sun);
    my (
        $second,     $minute,    $hour,
        $dayOfMonth, $month,     $yearOffset,
        $dayOfWeek,  $dayOfYear, $daylightSavings
    ) = localtime();
    my ($year)    = 1900 + $yearOffset;
    my ($theTime) = "${dayOfMonth}_$months[$month]";
    return $theTime;
}
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