Even without extensions or plugins, the signals will not always null when they are affected by real-time transpose or time stretch.
This is something I have found a while ago, and the issue is actually quite concerning.
I assume that when you duplicate the track, the Melodyne settings are also copied, so the audio on both tracks is outputted exactly the same, this is an exact copy, right ?
So, there is indeed a bug, but it originates from Cubase itself. I have spent more than thirty hours over two weeks to troubleshoot this issue, and have narrowed it down precisely.
If you have some time I invite you to read the full post carefully, though it could have been written a bit better but I can’t edit it anymore :