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Our server performed some updates last night and this morning we came in to find it stuck in a boot -> "Applying System Configurations" -> "Configuring Updates: Stage 3 of 3. 0%" -> reboot loop.

Safe Mode does not work, it still tries to configure the updates before going to the desktop.

I have the CD and have brought up the command line, but after a couple of hours of poking around and internet searches I haven't been able to produce any results. Any idea how to perform a "cancel update"/"restore"/"repair" from the CD command line?

Very similar problem: Windows Server 2008 is stuck at "configuring updates - stage 3 of 3 - 0% complete"

The link in one of the answers provided /some/ information, but no results. (http://support.microsoft.com/kb/949358/en-us)

I wasn't sure how to bump that post, so this may need to be merged.

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So, clicking F8 right after BIOS doesn't give you boot options? – l0c0b0x Feb 22 '12 at 19:42
    
It does, and I can select "Safe Mode" and "Last known good configuration" but they both still try to continue applying the update. – tehDorf Feb 22 '12 at 20:00
1  
Have you tried Googling this?: msmvps.com/blogs/bradley/archive/2010/03/25/… – l0c0b0x Feb 22 '12 at 20:22
    
I have not seen that article, but it looks promising. We're backing up some large files at the moment, but I'll try that as soon as those are finished. I've read other articles that said they did x/y/z and the problem was fixed, but those didn't work for us so I'll keep my fingers crossed. – tehDorf Feb 22 '12 at 20:47
    
@l0c0b0x That worked! Thank you! You should post that as an answer so I can accept it. – tehDorf Feb 22 '12 at 22:08
up vote 7 down vote accepted

Thank you to l0c0b0x for your help on this - I was able to successfully clear up this issue using the advice in his suggested blog post: http://blogs.msmvps.com/bradley/2010/03/26/fixing-a-bit-of-pending-xml/

Steps:

  1. Boot from the Windows Server 2008 CD.
  2. Select the Command Prompt option.
  3. Execute the command "del C:\Windows\winsxs\pending.xml".
  4. Reboot from HDD.

Warning:

@GaryRedshaw commented that after trying this, his sever started suffering from BSODs (see comment below). It goes without saying that any modifications to the Windows operating system files is inherently risky - please use your professional discretion when making such modifications.

Notes:

The original article talks about running the command window with elevated permissions and taking ownership of the pending.xml file before you can delete it. These steps were not necessary for me as I was able to do a straight delete on the file.

Windows may try to scare you when you reboot by displaying "Configuring Updates: Stage 3 of 3", but don't worry, it'll make it past it this time. (At least it did for me.)

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Just to let people know, I did this on a customer's system.. exact same symptoms, and the system began to blue screen.. Microsoft said we should never have deleted the pending.xml file. I would contact Microsoft support before doing this exercise. – Gary Redshaw May 18 at 18:01

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