The outer loop should be written like, more modern and safe (think embedded newlines).

my $csv_in  = Text::CSV_XS->new ({ binary => 1, auto_diag => 1 });
my $csv_out = Text::CSV_XS->new ({ binary => 1, auto_diag => 1, eol =>
+ "\n" });
open my $fh_old, "+<", $file or die Lava::Message ("Can't open origina
+l file: $file: $!");
open my $fh_new, ">",  $temp or die Lava::Message ("Can't open tempfil
+e file: $temp: $!");
$csv->getline ($fh_old); # skip first line. Header?. If empty line, 's
+calar <$fh_old>;' is a good option
while (my $row = $csv->getline ($fh_old)) {
    :
    :
    $csv_out->print ($fh_new, [ map { $row->[$_] } 0, 2, 1, 3, 0 ]);
    }
$csv_out->print ($fh_new, [ 0, 0.000, 0.000, 0.000 ]);
$csv_out->print ($fh_new, [ 0, 0.000, 0.000, 0.000, "END" ]);
close $_ for $fh_old, $fh_new;
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