#!/usr/bin/perl
use warnings;
use strict;

use XML::LibXML;


my $new_values_file = shift;

my $dom = 'XML::LibXML'->load_xml(IO => *STDIN);

open my $in, '<', $new_values_file or die "$new_values_file: $!";
while (<$in>) {
    chomp;
    my ($two) = $dom->findnodes("/root/one[$.]/two[\@origin='a']");
    $two->removeChildNodes if $two->findnodes('text()');
    $two->appendText($_);
}
print $dom;