You can send up to 16 bytes in one packet, but you might only want to change three bytes. The datalength says how many bytes to change,

Yes, that is what I assumed, but your code always sets the datalength value to 16.

You might try it like this:

while ( my $line = <$ifh> ) {
    # Ignore comments
    next if $line =~ /^#/;

    # Split elements and do some very basic validation
    my ( $runonce, $hour, $minute, $second, $command, $offset, @values
+ ) = split ' ', $line;
    @values or croak( "Line $.: has not enough values: $line\n" );

    # Turn the given command NAME into the correct command NUMBER
    defined $commandmap{ $command } or croak( "Line $.: Unknown comman
+d $command\n" );
    my $numcommand = $commandmap{ $command };

    # Internally in the Radioduino, the "runonce" flag also serves
    # as "invalid record" flag, so turn the plaintext 0/1 boolean into
+ the correct number
    my $mode = $runonce + 1;

    # Turn everything into binary
    my $event = pack 'C C C C n C C C16',
        $mode,
        $hour,
        $minute,
        $second,
        $offset,
        $numcommand,
        scalar @values,
        @values, ( 0 ) x 16;

    # Write binary entry to file
    print $ofh $event;

    print $line, "\n";
    }
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