Hi @FunMiles!
After shutting down OpenHAB, then unplugging the device, pairing with new devices, re-plugging the usb device and starting OH again, it sometimes does not recover the existing USB setting for some reason.
Have you checked if, in those cases, the port of the USB device has changed? In Linux, if you unplug and re-plug a USB device, it’s very common to see that the OS gives the device a new port: from /dev/ttyACM0 to /dev/ttyACM1. As the Z-Wave thing is configured to listen on /dev/ttyACM0, it won’t recognize the new /dev/ttyAMC1 device and your Z-Wave network won’t work. You have three solutions:
- Instead of restarting openHAB, reboot your whole device everytime you disconnect the USB controller. On a clean restart, the controller will always get the /dev/ttyACM0 port.
- In Paper UI → Configuration → Things → Z-Wave controller → Edit button (Pencil) → Serial Port → “/dev/ttyAMC1”. But this won’t work for long, because next time the controller will get the “/dev/ttyACM0” port and you will have to change it again.
- Give the USB device a fixed port identifier with udev rules. General information: http://hintshop.ludvig.co.nz/show/persistent-names-usb-serial-devices/ openHAB info: Raspberry Pi - Make serial USB ports persistent via symlinks
You should never delete and create a new Z-Wave controller thing, because, as you have seen, the individual Z-Wave nodes are linked to the controller through the thing id. Let’s see if any of the proposed solutions works for you. The simplest one is the first one, but the best solution is the last one. If you have any problem, don’t hesitate to ask 
Best regards,
Aitor