Before xml removal:

<item1/>
<item2/>
<item3/>

After removing item2:

<item1/>

<item3/>

Here is the sample code snippet (And yes, I pull the list using XML::Simple.)

my $manifesto = XMLin($google_manifest);
foreach my $project (sort keys %{$manifesto->{'project'}}){
 if ($project){
  $project = 'a/aosp/' . $project;
  print "Project = $project \n";
  my $query1 = '//project[@name = "' . $project . '"]';
  my ($node) = $doc->findnodes($query1);
  if ($node){
   $node->unbindNode();
  }
 }
}
print $doc->toFile($new_manifest);