Thank you for posting your question.
When you deploy, our deployment tracker sends the status of the deployment from the target machine to the console machine using TCP port 3121. If anything stops the traffic during the deployment whatever stage the deployment may be at, the status will remain the same in the deployment tracker no matter what you do as that is the permanent deployment result. Therefore, you are not in danger of rebooting if you have already rebooted, but the deployment tracker will stay the same.
So how do I trouble shoot the issue? Seems like you said, it was working then stopped.
Thank you for creating a case and reviewing this issue with me.
To review, we found that the deployment worked through three patches and then something hung it. I believe that Windows Automatic Updates Best Practice: Windows Automatic Updates or Antivirus Exclusions For Patch Deployments could very well be the cause of this, but at any rate, we found that your deployment tracker was working correctly and there was no actual pending reboot since the machines had already been rebooted.