I'm a bit confused. Are you using a Pi? If so you would be updating everything with sudo apt update and sudo apt upgrade. If it's failing to update the Duet because it's on a beta firmware you can manually update the Duet over USB to get back in sync.
@dc42 The problem is that when trying to print via OctoPrint there's an error being thrown Too many consecutive timeouts, printer still connected and alive? So I can't use OctoPrint with the Duet board. It seems like this problem is happening specifically when G29 is running.
There is config in octoprint to tell it about "long running commands" that will solve this problem for you.