#!/usr/bin/perl

use strict;
use warnings;
use Tie::File;

my $file = '/path/to/file';

tie my @lines, 'Tie::File', $file or die $!;
for my $index ( reverse 0 .. $#lines ) {
    next unless $index % 2;
    splice @lines, $index, 1;
}
untie @lines;