@lewis.heidrick’s advice is good. The PC Controller is. part of the free Silicon Labs’ Simplicity Studio software, and I have the USB stick from SiLabs. But you may be able to remove them without it.
You haven’t provided screenshots of your ghost nodes, so I can only speculate based on my memory. You have to click the repair button a few times (wait about a minute between clicks, you can see the progress in the logs as hub tries to access the non-existent node) before the hub decides that the node has failed. When the node indicates FAILED, then the Remove button can be used to remove the node.
See if that helps. The USB Z-stick is guaranteed to work.
Here is a guide:
