Maybe there is an error? The AnyEvent::i3 documentation mentions that ->command returns a result:

use Data::Dumper;
sub handle {
  my($data)=@_;

  if($data->{change} eq "empty") {
    print "empty workspace!!\n";
    my $switched; $switched = $i3->command("workspace 1")->cb(sub {
        my( $reply ) = @_;
        print "Switched back to workspace 1\n";
        undef $switched;
        use Data::Dumper;
        print Dumper $reply;
    });
  }
}
[download]

This is what I get:

empty workspace!!
Switched back to workspace 1
$VAR1 = bless( {
                 '_ae_sent' => [
                                 [
                                   {
                                     'success' => bless( do{\(my $o = 
+1)}, 'JSON::PP::Boolean' )
                                   }
                                 ]
                               ]
               }, 'AnyEvent::CondVar' );
[download]

However no switching occurs. No clue what is going on there...

So, the i3 API tells you that all is well. This sounds more like a problem with i3 to me. Maybe consider delaying the switching a bit. Set a timer (AnyEvent->timer(after => 3, sub {...}) and trigger the desktop switch from that timed callback instead of triggering it directly.