Just putting this in for anyone who still has the issue after restarting the VM instance.
You will also need to update your name record with the new IP address that Google Cloud assigns following your upgrade. My email came back up, but not website.
Copy the new external IP (ephemeral) address from the Compute section (for the VM instance for the domain)
Go to Network Services > Cloud DNS and edit and past the new IP address into the A record, save. (I stopped the VM instance before updating the A record, and restarted after, not sure if it was needed)
But it solved my issue and my website is back up.