Repairing a Corrupt Multi-Boot Startup

Mike Halsey MVP
Mar 21, 2011
Updated • Dec 27, 2012

I get all manner of emails in my weekly mailbag, but one of the most common is about repairing a corrupt startup. I have a video on YouTube explaining how to use the Startup Repair features in Windows 7 (this will also apply to Windows Vista and Windows Server 2003 and 2008) but what happens if you have a multi-boot system?

I received an email this weekend from someone who was running Vista, Windows 7 and Windows Server 2008 in a multi-boot system. You might be surprised but this system actually makes it relatively easy to rescue a multi-boot system. But what if you're running Windows XP or Linux and how would you rescue that?

Identifying the Boot files

On all new Windows systems you'll find that in order to be able to install an operating system such as Windows XP or Linux, you'll have to install that before Windows Vista or Windows 7. This is because of the new secure windows boot system. If you right-click on Computer in the Start Menu and select Manage from the context menu that appears you will bring up the Computer Management Console. Here you can click on Disk Management in the left-hand panel to see the hard disks and partitions in your computer.

You should have a 100Mb partition called System Reserved. This is where Windows keeps all its boot information. If you do not have this partition and are running Vista, Windows 7 or Windows Server then that boot information will be store on the Windows partition itself (whichever one of these three you installed first). Do note though that this partition might even be on a separate drive to your copy of Windows.
computer management

Backing up the Boot files

The best thing to do when everything is working is to create a full backup of this System Reserved partition. If you use the System Image Backup feature in Vista, Windows 7 or Windows Server 2003 or 2008 to create a full backup of your copy of Windows then this partition will automatically be backed up and will be restored when you restore that image of Windows (any of them in fact if you have more than one).

You could also use a third-party disk imaging tool such as Symantec Ghost to back up just the System Reserved partition and even though these can be expensive, a search of computer magazine cover disks or a trip to should reveal one you can use for free. You should create an image of this boot partition and keep it somewhere safe on your computer.

With this backup should your computer's boot files become corrupt, simply restoring the System Image backup will reset everything and get your computer operating again.

Manually Backing up and Rebuilding the BCD boot file

I have another video which explains how to manually rebuild the boot files in Windows which you can see here. You could run through this and find that it successfully repairs the boot files. If you follow the instructions to get as far as making a backup copy of the BCD boot file, you can then copy this file out to another safe place on your computer when it's all working. This means that you can copy it back should it become corrupt.

This method offers no guarantee of repair success but in conjunction with the other BDCEDIT commands I talk about in the video, offers you a fair chance of success at getting your system working again.

Repairing a Multi-Boot Startup

Okay, so let's assume now that you don't have one of these backups and your boot files are corrupt, how can you repair them? The only way to do this now is to repair them in order of ageso far as the boot systems go. This means that you should start first with Windows XP or Linux and then do Windows Vista or Windows Server 2003 and Windows 7 or Windows Server 2008 last of all.

If you are just using Windows XP and Linux then the XP recovery console will be able to help you rescue your system, but this won't work if you have Windows Vista or later installed as this introduced a new boot system that's incompatible with XP and Linux.

You'll need to reinstall the older OSes (XP or Linux, Yes I know Linux isn't old, only its boot system!) as these operating systems don't come with a startup repair system like newer versions of Windows. You can perform a fresh install over the top of your existing copy but do not format the partition. This will copy all your files in XP into a Windows.old folder from which you will be able to recover files and data.

With the newer copies of Windows you can then start by trying Startup repair again though at this point it's probably not going to work. When time comes to reinstall try formatting the System Reserved partition ONCE and only on the first install. Windows XP and Linux won't have used it so you can clean it out to start afresh. Then reinstall in the same way as with XP by performing a fresh install over the top of your existing copy without formatting the drive. This will put your old copy of Windows into a Windows.old folder from which you can rescue files.

The first time you install Windows Vista, Windows 7 or Windows Server 2003 or 2008 this boot partition will be rebuilt and it will include the relevant information for XP and Linux if you have them installed as well. NOTE this time Windows may put the system reserved partition in a different place and has even been known to put it on other hard drives containing files or data. If this is the case you can move it, and I'll write this up in a separate article this week.

If you do keep your files and data on a separate hard disk or partition then you can feel free to format the drives or partitions before reinstalling your copies of Windows as this will create nice clean installation for you and should repair any problems with the partition itself.


This isn't an easy or quick process by any stretch of the imagination, however in the case of dual-boot systems that are either simple or complex, it ought to get you up and running again. Good luck.


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  1. Howgeekis said on May 24, 2020 at 2:08 am

    LO: Right. That s really, really interesting. So talk about what specifically you guys found, what was the feature that was in focus that these different attacks kind of stemmed from?

  2. edmar said on March 22, 2011 at 5:59 am

    I wonder how many people are still using Windows XP and Windows 7 in dual boot. If I am one of them and Windows XP got corrupted, I will just junk it and repair Windows 7 and stay with it.

  3. Locutus said on March 21, 2011 at 11:36 am

    Why happened to
    bootcfg /rebuild
    For Windows XP?

    1. Mike Halsey (MVP) said on March 21, 2011 at 12:25 pm

      @Locutus I’m assuming that people won’t be just running Windows XP as it’s now been out for 10 years. Much more likely they’ll be dual-booting it with Windows 7.

      In this circumstance the XP Recovery Console won’t help as Vista introduced a new boot loader system.

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