You are calling $template->param() multiple times within the perl loops, which will overwrite any previous settings. And you are calling $template->param(SCHEDULE_ROWS ...) inside an if block, so if that test returns false it won't be called at all - hence the error.

Here is a trimmed down version to show the logic required:

for my $customer (keys %$bi) {
    for my $domain (keys %{$bi->{$customer}}) {
        my %customer_domain_data;
        my @schedule_rows_loop;
        for my $host (keys %{$bi->{$customer}->{$domain}}) {
            if (defined $schedule) {
                for my $dif_schedule(@schedule) {
                    push (@schedule_rows_loop, \%schedule_rows_data);
                }
            }    
        }
        $customer_domain_data{SCHEDULE_ROWS} = \@schedule_rows_loop;
        push (@customer_domain_loop, \%customer_domain_data);
    }
}
$template->param(CUSTOMER_DOMAIN => \@customer_domain_loop);
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