v5.0.0 of the 2factor authentication plugin has been published. It now allows for concurrent second factors, so you can have both a hardware key and an authenticator app in use at the same time.
When challenged, you can use either option to verify your identity.
@Shaun when 0.5.0 is released, their will be full documentation, but the process will be something along the lines of
git checkout v0.5.x
git pull
./nodebb upgrade
But their will be an announcement about all of that and how to update when it's ready. If you have any other issues with plugins etc, feel free to create a topic. 👍