I was using Z-Wave PC Controller 5 to remove ghost nodes from a Z-Stick. With version 5 you just need to go into the “Network Management” option, click the node, click “Is Failed”, then it should turn red. Once red you can click “Remove Failed” (fuller explanation here).
However two of my nodes which I knew no longer existed on the network would repeatedly fail the NOP test but never go red, meaning you couldn’t remove them. The solution was to click the “Topology Map” and note the failed nodes were apparently routing between each other. Fortunately I had one of those failed nodes still available, so I plugged it back in then in “Network Management” did a successful “Is Failed” test then “Neighbors Update”. A check in “Topology Map” then showed it no longer considered the other failed node as a neighbor. As soon as that happened the “Is Failed” test for the remaining problematic node failed and made that node red and able to be deleted.
TLDR: If you have trouble removing a node, check its neighbors in the topology map and do a “Neighbors Update” for such neighbors.