I'm having the same problem referenced at https://social.technet.microsoft.com/Forums/windowsserver/en-US/73e91012-c779-4a41-9bd5-02ae4db16a67/2012r2-hyperv-guest-stuck-updating-your-system-6?forum=winserver8gen. I started with a 2012 R2 VM that was last used in May, booted it yesterday, and applied the 121 pending patches from WU. Now it hangs at 6% when restarting.
Steps I've tried:
- From the recovery prompt, removing c:\windows\winsxs\pending.xml. File wasn't present on the target system.
- Running the script from https://gallery.technet.microsoft.com/ScriptCenter/5b4a7114-218b-466c-a9c1-7eb2f725e707/ on the host. The cert shows as correct in the registry.
- Disabling and re-enabling secure boot.
- Running dism.exe /image:C:\ /cleanup-image /revertpendingactions, which produced errors but didn't fix the problem.