open my $fh, '+<:utf8', 'file.in.xml' or die $!;
my $line = <$fh>;
$line=~s/<\?xml.+encoding="\Kutf-16"/utf-8" /
    or die "didn't match line: '$line'";
seek $fh,0,0 or die $!;
print $fh $line;
close $fh;

##</code><code>##

perl -v

This is perl 5, version 24, subversion 0 (v5.24.0) built for MSWin32-x64-multi-thread

##</code><code>##

#!/usr/bin/perl
use 5.024;
use strict;
use warnings;
use XML::Twig;

open (my $OFILE, '>:utf8', 'file.out.xml') or die "$!\n$^E";

my $t = XML::Twig->new(
  twig_handlers => {
    '/keys/key' => sub { $_[0]->flush($OFILE); },
  },
  
  output_encoding => 'utf-8',
  pretty_print => 'indented',
  comments     => 'drop',  # remove any comments
);

$t->safe_parse(\*DATA);
if ( $@ ) {
  die "Error occured in XML data\n\n$@";
}

close $OFILE;

__DATA__
<?xml version="1.0" encoding="utf-16"?>
<keys>
  <!-- One hen -->
  <key>45646fa8-32e5-494c-93ff-0f00281fc2d6</key>
  <!-- Two ducks -->
  <key>b6bdc46f-3275-4312-bbbd-3e375208d05f</key>
  <!-- Three squawking geese -->
  <key>e5a37cf0-1f69-41a8-899c-23454600894a</key>
  <!-- Four limerick oysters -->
  <key>b6287f3d-f70c-498d-8360-5a2d8e863ab3</key>
  <!-- Five corpulent porpoises -->
  <key>118be380-5e69-47d4-81c6-756c34334936</key>
  <!-- Six pair of Don Alverzo's tweezers -->
  <key>46f9dd5b-d0e9-4f8f-a559-f698bea561fa</key>
  <!-- Seven thousand Macedonians in full battle
  array -->
  <key>9627058f-29f0-4263-8978-fc77ac2fe0a3</key>
  <!-- Eight brass monkeys from the ancient
  sacred crypts of Egypt -->
  <key>6038d393-ba81-423e-8429-01406779ff9e</key>
  <!-- Nine apathetic, sympathetic, diabetic old
  men on roller skates, with a marked propensity
  towards procrastination and sloth -->
  <key>5a67c3f0-ea6f-427c-bc3a-86fdb31fd117</key>
  <!-- Ten lyrical, spherical, diabolical
  denizens of the deep who stalk about the
  corners of the cove all at the same time. -->
  <key>7ac8b1d8-ff60-4b55-8fe0-ea809d9f5b02</key>
</keys>