Copying Hard Disks with Bootable Windows GPT Partitions Using Linux

This is just a placeholder blog post. I keep intending to do a proper blog post on this topic, but I never get around to it. Unfortunately, I always forget the steps I need to do when I'm in the middle of copying my hard disks and can't consult my notes, so I'm going to just put some placeholder notes here and flesh them out properly later.

Note: Copying hard disks is tricky. I disclaim all responsibility if you use these steps and you lose data or your BIOS becomes corrupted or whatever. This blog post mainly serves as notes to myself.

About GPT Partitions
I still don't fully understand how a modern UEFI system boots from GPT partitions. I think with GPT and UEFI, your hard disk contains multiple partitions. One of them is a FAT partition that's special because it contains some boot loader programs that contain the instructions needed to load an OS from one of the other partitions. That partition is called the EFI System Partition. The UEFI BIOS of a computer will start Windows in two ways

1. Usually, the BIOS stores the specific UUID label of the boot EFI System Partition and the name of the boot loader program on that partition to load. The BIOS can then quickly load the boot loader and then continue on to load the OS.
2. When you first install Windows, the BIOS doesn't have that information yet, so the BIOS is able to find the EFI System Partition on the hard disk itself, find the default Windows boot loader on that partition, and then run that to start Windows.

Why It's Tricky Copying Windows

Copying Windows GPT partitions is hard because

• Windows makes it hard to copy Windows partitions
• the bootloader program on the FAT partition has to be changed to load things from the new partition
• the BIOS has to be changed to know about the new bootloader

Steps for Doing the Copy

By default, Windows is configured with some settings that lets it keep the file system in an inconsistent state on shutdown (in order to have faster shutdowns and bootups), which is a bad time to copy it. I tried various methods for disabling that, but the only reliable approach seems to be to turn off hibernation entirely. You need to start a command prompt in Administrator mode. Then run

     powercfg -h off

If you're copying to a smaller hard disk, you might want to use Windows Disk Management (right-click "This PC", choose "Manage", then choose "Drive Management" under the "Storage" category on the left) to shrink your partitions in advance, but that usually never works, and Linux can shrink your partitions anyway.

Also make sure that you have a bootable version of a Windows rescue CD or the Windows installation media.

Now, you can start-up Linux to start copying your hard disk. I always use the GParted LiveCD to do this. GParted can be slow to start-up because it scans through all your hard disks very slowly to find all the partitions. I think it might also do some really slow thing with Windows partitions as well. That scanning step gets slower the bigger your hard disk is too. But I've found it to be pretty reliable. Use this to copy your partitions to the new hard disk.

msftres Partition

You may find that your hard disk has a msftres (Microsoft reserved) partition. GParted is unable to copy this partition. It is not necessary to copy the partition. It is just a partition that Microsoft reserved so that if you ever install Windows Bitlocker disk encryption, Microsoft can store the decryption code there. If you do want to keep this msftres partition, you can manually create one. First, copy all the partitions before the msftres partition. Then boot into the Windows installation CD (you did remember to make one, right?). Go into the Advanced Repair settings and get to the command prompt. Then use the "diskpart" program to create an msftres partition. I forget the exact steps. You can type stuff like "help," "help select disk," "help list partition," "help create partition msr" or something to get the exact commands you need. But you need to select the new hard disk, then use something like "create partition msr size=128" to create a 128MB msftres partition. Then, you can reboot into GParted to copy the rest of the partitions.

 

Update 2020-9-22:

> list disk

> select disk n

> list partition

> create partition msr size=128

GParted Fix-ups

GParted will make the copied partitions have the exact same IDs as the old partitions. This can be a problem if you keep both the new hard disk and the old hard disk in the same computer (e.g. when moving from a hard disk to an SSD, you might want to keep the old hard disk around in the same computer as a backup). It's not clear which boot partition the BIOS will use when starting up. And when Windows is loaded, the wrong one can potentially start up. And even if the right one starts up, the wrong partition might end up being mapped to the C drive. To be safe, if you intend on keeping both hard disks in your system, you should go in and change the UUIDs of all the partitions on either the new drive or the old drive. I'm not 100% sure about Windows recovery partitions. To have the recovery work properly on the new hard disk, it might be better to have it keep the same UUID, so then generating new UUIDs for the old hard disk may be better. But I could never get that recovery partition to work properly anyway, and I would rather have at least one proper working copy of my hard disk in case the copy goes bad, so maybe it's better to generate new UUIDs for the new hard disk.

GParted also often doesn't copy the partition labels and flags correctly. You can go in and set those manually so that they're the same on both disks. I've forgotten to do this before, and everything still seemed to work, so this might not be necessary.

Update UEFI BIOS with Location of Bootloader

Now that Windows is copied, you need to update the BIOS with which bootloader to use on start-up. If you didn't change the UUIDs of the newly copied partitions, then this might not be necessary since the existing BIOS entry for the location of the old bootloader should still work. You might need to swap hard drive cables to ensure that the new hard drive takes over the old drive number from the old hard drive. Or maybe not? 

If you did change the UUID of the boot partition, then this is definitely necessary. Open a Linux terminal. Become root by using "sudo bash". Then use the "efibootmgr" program to create the necessary entries. 

 

Update 2020-9-22:

> efibootmgr or efibootmgr -v 

to list boot entries

> efibootmgr -o i,j,k

to change boot order e.g. efibootmgr -o 2,1,3

(check man pages for other commands)

I can never figure out how to create new BIOS EFI entries using efibootmgr, so I sometimes try to use some other approach to create these new entries. Sometimes, if you start up your system with only your new hard disk, the BIOS won't find the default bootloader, so it will default to searching for the Windows bootloader itself, and it will then add an entry for it in the BIOS itself. Or you can try starting a Windows Recovery CD or installation DVD, going to the command-line repair tools, and trying to use "bcdedit", "bcdboot", or "bootrec /rebuildbcd" to do this. I'm not sure what these programs do, but I think one of them will create a new EFI BIOS entry for the bootloader partition.

Once you have an EFI entry in the BIOS for the bootloader, you can go back to using "efibootmgr" to rearrange the order of your boot entries so that it comes first, which is a lot easier than creating a new entry from scratch.

Update Bootloader with New Location of Windows Partition

Now the BIOS can find the bootloader to start loading Windows, but the bootloader may not point to the correct partition to actually start the OS. Again, you can try starting a Windows Recovery CD or installation DVD, going to the command-line repair tools, and try to use "bcdedit", "bcdboot", or "bootrec /rebuildbcd" to do this. Again, I'm not sure what these programs do. I don't actually know what the BCD is, and the Microsoft documentation is very vague on that fact. I think it refers mostly to the configuration files for the bootloader on the EFI FAT system partition, but I don't know. Sometimes, everything has gone bad, and you need to use "bcdedit" to start a completely new BCD store. In any case, after randomly running some combination of those programs, Windows will somehow fix itself and become bootable.

Checking Windows

When you do manage to successfully boot into Windows again, going into Drive Management to make sure that the correct drive is listed as your boot drive and that it is the C drive. You might also need to manually remove drive letters from some of your recovery drives and other drives. Don't forget to reenable hibernation by going to the command prompt as an administrator and using

     powercfg -h on

Fixing Up Your Linux Bootloader

I normally use Windows, but I keep a copy of Linux on my drives for occasional use. Normally, I just let Linux install a boot loader into the EFI system partition and add an entry to the BIOS. I change the boot order to normally boot to Windows, but I use the "boot from alternate drive" key on startup to show all the EFI boot entries, and then I manually choose the Linux one. 

After copying a Linux partition to a new hard disk, you have to reinstall the grub bootloader on the EFI system partition to point to the new Linux partition. Reinstalling grub is mostly impossible, so I find it easier to simply reinstall Linux over the old version (I keep my Linux data on a separate /home partition, so that it's safe to do that without losing data).