@date1 = ($dt[0], $dt[1], $dt[2], $dt[3], $dt[4], $dt[5]);
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This kind of thing is redundant and error-prone. That's why we have array slices!

@date1 = @dt[0..5];
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Another redundancy:

    chomp($line1);
    my @mg1 = split(/,/, $line1);
    my $line2 = <IN>;
    chomp($line2);
    my @mg2 = split(/,/, $line2);
    my $line3 = <IN>;
    chomp($line3);
    ...
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You've replaced it with a loop that calls Add_Delta_DHMS on every line, not just once per twelve lines, so it's not equivalent at all. I would tend to write something like this:

my ($sum) = split /,/, $line;
for (2..12) {
   my ($val) = split /,/, <IN>;
   $sum += $val;
}
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