This has been discussed four or five times in detail in The various threads on zwave repairs, what exactly were you confused about?
The hub has a list of all known devices. During a Z wave repair it attempts to contact each device and ask it to update its neighbor table. It’s a call and response format command. (It uses the normal mesh system, so the messages do get passed along in both directions using repeaters.) If it doesn’t get a response, then it notes the error. I’m not sure why that would be “counterintuitive.“
The following thread goes into excruciating detail if you need more than that. 