I would try changing to your virtual env and manually installing python_openzwave to see if that fixes it. pip3 install --upgrade python_openzwave==0.4.9
I would shut down the HA service before installing.
Weeks ago my installation in venv was also broken. Reason for me was that in the end of 2017 I installed manually a python 3.6 version. In meantime I did a OS - update and some dependencies got lost (to debian stretch) because default python in debian 9 is python 3.5.
My solution was reinstalling HA after saving configuration. I just deleted the old pyhton 3.6 binaries before new installation of HA.
I also had this issue, but I changed my usb zwave controller device ID in configuration.yaml and it worked, for some reason it sometimes sees it in as devACM0, 1 or 2 when restarting the Ubuntu VM…