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I did a Disk Cleanup on my Server 2008 R2. It said it was going to delete a bunch of windows update files which had built up over many updates. When I restarted, windows tried configuring an update before launching (the grey screen with a % update tracker) but got stuck.

I cant launch in safe mode, it just tries to update anyways and gets stuck.

I tried using repair disk Cmd prompt to delete pending.xml but there was no windows installation on C drive (huh????)

With a little poking around and using the explorer on the repair disk, it turns out that my system has moved to drive G, and C drive is now called "System Reserved" and has just a boot folder and a couple of other almost empty folders.

My theory is that this is what Windows does when configuring updates, it temporarily creates a new partition, renames it to C: (while renaming the system partition to G:) so that it can configure or something. Unfortunately, because Disk Cleanup deleted some files it wasnt supposed to, Windows thinks its supposed to update but for some reason cant, maybe because something is corrupt or it is missing files or something.

So... how do I reverse this? I did make a backup of my C drive about a month ago. But I would rather try to preserve my changes since then. Anyone know if I can cancel this partition split? Either delete C and force a boot from G or somehow make G into C again? Anyone have any experience with this? Lol... PLZ HALP! :)

My guess is I will need to delete the boot folder in the "System Reserved" partition and rebuild a boot folder in my system partition. Can anyone confirm if this is what I should be looking into?

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    You system hasn't move to G:, it is mounted as G: while you are in the repair disk.
    – Drifter104
    Dec 17, 2015 at 11:04
  • The "system reserved" disk is always there, it contains the boot loader files. In a running system, it is a volume without a drive letter, so it does not appear in Windows Explorer's view. In a rescue system, every volume / partition gets a drive letter (and a possibly different one, too). There is nothing wrong with that, so your assumption is incorrect. This does not fix your system yet, though.
    – the-wabbit
    Dec 17, 2015 at 11:05
  • Just boot off the DVD and do the repair boot option at least twice.
    – JamesRyan
    Dec 17, 2015 at 11:09
  • Ok thanks, that helps. Im no longer stuck in a "configuring updates" screen. I did a startup repair a couple of times but now when I try to reboot into my system it says bootmgr missing. Also, I dont know if this is related, but when I try some of the other options on the repair disk, such as "Refresh your PC" I get the message "The drive where Windows is installed is locked. Unlock the drive and try again."
    – Leo Fabrikant
    Dec 17, 2015 at 15:35
  • Ok I see... So i found online you can fix the "Bootmgr missing" by activating the system partition in cmd prompt. It looks like startup repair deactivates it. When I did that, I am back to the configuring windows updates page stuck at 35%. So it appears that my system partition is broken, stuck in an update. Any one know how I can reset it?
    – Leo Fabrikant
    Dec 17, 2015 at 15:45

2 Answers 2

Reset to default
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  1. Disk Cleanup can take 1 to 4 hours. It's NORMAL to sit at 100% Configuring updates after rebooting. If you can't wait that long, don't run Disk Cleanup.
  2. You should always have a current backup image of your server so you can easily recover if necessary. We use Macrium Reflect Server.
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  • Just ran into this issue. If you are stuck you can use psexec or pskill to kill the TrustedInstaller.exe process on the problematic server. This will get you past the "configuring windows update 100% complete" screen.
    – qroberts
    Dec 15, 2021 at 22:36
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My guess is I will need to delete the boot folder in the "System Reserved" partition [...]

I hereby confirm, that this is NOT the way to do it. The reserved partition is there to boot (NTLDR) from and that's good; don't worry about the disk labels, the Windows kernel knows how to handle this (usually the boot partition does not get any drive letters, so you can savely delete THE LETTER).

[...] but got stuck [...]

I have seen a lot of "stuck" machines that were not really stuck. Just give it (a lot) more time - I have waited up to 20 hours for a (slow) machine to come up again.

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