Thank you for the quick responses. Maybe (not so) coincidently, the complexity of that exact dropbox PDF file is what led me to post in this forum. My fear is that, given they technically are part of my network, I will continually fight with those ghost nodes popping up. Even after following the steps in that document.
As for the companion switches, currently the circuits are setup as:
Leviton DZ6HD-1BZ / Leviton DD00R-DLZ (master/slave). No functionality issues relating to the multilocation circuits.
My reliability problems are VERY intermittent and revolve around completion of basic rules, slow node response times (greater than 10 seconds) and loss of connection to certain nodes on the network for a few minutes or more.
I will try the manual removal via the Hub > Settings > Z-Wave Details, and a hard reboot as mentioned: