Try:
- Shutdown home assistant
- Follow the USB controller instructions for including devices (using the built in button on the controller stick)
- Reconnect the controller
- Heal your network which may take some time
and then see how you go. If you can, try a visualization such as this one to help you understand the topology of your network.
Don’t try to do them all at once, and be patient when the zwave network starts up as it can take some time (minutes) for the network nodes to be found.