Cloned HDD now neither drive will boot

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roma247

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Sep 25, 2014
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Used Clonezilla to clone my 1TB HDD to a new 2TB HDD (Win 7 Pro OS) with a USB mount. I did have it clone the boot loader, and I used option -k1 to enlarge the partition. So far as I can tell, it completed without errors.

Unfortunately, my son tried to boot from the new drive while both were still hooked up. It tells us that BOOTMGR is missing.

We mounted the new disk and unhooked the old one.
We tried putting in the original OS installation disk and running Startup Repair. Nothing.

Tried command prompt > Bootrec /RebuildBcd. Nothing.

command prompt > fix mbr. Nothing.

Tried hooking both drives up to my laptop to verify that the files are indeed there, that the drives are active, etc. Everything checks out (Although the new drive still thinks it's 1TB, so -k1 didn't work...)

I am running out of options here. I can't boot from either drive, so I can't retry the cloning process without fixing the boot error in the original HDD. Is there anything at all that can be done to salvage this wreck, besides just starting from scratch with a fresh install that will take me a week to complete?
 
Solution
SkyNetRising
Drive letters in recovery environment do not matter. They have no relation to drive letters, when you boot into windows.
Ok - one more option.
Delete and recreate 78MB partition.
  • diskpart
    list disk
    select disk 0
    list partition
    select partition 1 (make sure you select the right partition - 78MB)
    delete partition override
    create partition primary
    format fs=ntfs quick
    active
    assign letter=o
Then recreate bcd store
  • bcdboot d:\windows /s o:
d - volume letter of os partition, o - volume letter of bootloader partition
Then perform startup repair.
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First , avoid using clonezilla ...

if you want a Free software , use Paragon backup and recovery , it is super good.

https://www.paragon-software.com/home/br-free/


as for clonezilla , try goto bios and check Legacy mode instead of UEFI .. and see if the drive boots.
 
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Can you clarify what you mean? I've gone into the BIOS of the cloned drive and am finding nothing matching what you said above. Do you mean I should check those settings in Clonezilla?

I apologize if I'm being daft, but I'm confused.
 
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Connect new drive only.
Boot from windows installation media (has to be same OS version as installed).
Go to command prompt and execute:
  • bcdboot x:\windows
(x - drive letter of OS partition, it may be c: , may be d: . You can verify drive letter with) :
  • diskpart
    list volume
 
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goto the System bios . and choose the boot mode , you will find Legacy and UEFI ,

some times cloning/images software chooses the wrong method and when you boot in the wrong method , it will not boot.

so try Legacy mode first and see.

Just try it for a fast way ..

UEFI is better . always use UEFI in the future .

sadly ,
at the end you will need to install fresh I think...
 
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Have you experienced that? Seems unlikely.
Cloning makes exact copy. In disk clone mode it should clone MBR to MBR and GPT to GPT.

Only if you cloned in partition to partition mode and source/destination drives had different partitioning schemes, only then that could happen.
 
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if the software does not support UEFI yes it will happen. I dont know why but it happened to me with clonezilla thats why I hate that software ... I only use Paragon now for free , and Arconis true image for paid.
 
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Thanks. OK, we did this. It copied the boot files successfully but when we tried to boot, we got the same "Bootmgr missing" message.

Here's a twist: I seem to recall that when I installed the first time, I put the OS in its own partition. This partition shows up without a drive name or letter, and in diskpart it says it is hidden. (Though the main partition is named OS)

Could this be the problem? And is there a way to fix it?

Again, sorry for being dopey, I'm no computer expert but I'm not a total dummy either. But I'm clearly out of my depth here.
 
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I've looked everywhere in the System bios and cannot find boot mode or Legacy or UEFI. Theres a boot tab but it doesn't have this.

I have cloned a disk before using this exact method. Don't know why it's totally messed up this time... 🙁
 
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start installing fresh windows , the time you are wasting trying to fix it is more than the time needed for new fresh install.

format the 2TB and start installing ... it will end in 1 hour max ..

after that use better software for disk image. and by the way , make disk image file as well . for later , cloning is not good if your system gets infected , you will be cloning viruses . make a clean disk image much more better. and avoid zilla stuff lol
 
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SOOO not true. Add to that years worth of Windows Updates, the huge amounts of software and hardware I'll have to reinstall...it will take me a week to get back up and running.
 
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Yep. Several times. It says everything is A-OK, but when we try to start up, it still says BOOTMGR missing.


Your wish is my command.
open


I added an image but it doesn't appear to be showing up. If you can't see that, you can try this link:
photo of diskpart
 
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https://support.microsoft.com/en-us/help/2622803/windows-error-message-bootmgr-is-missing-press-ctrl-alt-del-to-restart

Okay , if trying to fix it does not work , here is some thing to try ,

1- fresh install
2-Copy EVERYTHING from the old Drive to the new one (overwrite)

try it as a last resort,

 
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Yep, tried everything on that page. Nothing worked.



Actually since posting this message we were able to get the original HDD to boot using Startup Repair a bunch of times. Not sure why it will work with the original HDD but not the new one...

But at least that makes the above a possibility...

...or I suppose I could try the recloning with a different program. (Though not sure of the stability?)
 
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So - 3 partitions: 78MB, 35GB, 1827GB. Witch of those contain OS, bootloader?
Can you post also photo of command:
  • diskpart
    list volume

My guess would be - 78MB for bootloader, 35GB for OS. 35GB seems kinda small for windows 7.
 
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The way they show up in Disk Management when I mount this drive via USB:
The first is the hidden partition.
The second is labeled Recovery.
The third is labeled OS.

This first partition is the one I thought I created myself for the OS, but now as I see it is labeled OEM, that would be the partition created automatically by windows upon install. So my memory must be faulty (probably I considered creating a partition for the OS and decided against it) and the third must be where the bootloader is? But we've tried that and it didn't work.

Photo of list volume:
open

list volume
 
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OK, we tried doing the above, and it will select volume 4 but when we try to clear the attribute hidden, it says "the object is not found." It will set it to active, but it won't unhide it.

I compared what I see in the current list volume to that of another functioning computer. In that one, in the column under "info", the RECOVERY volume is hidden (as it is supposed to be) and the OS Volume is marked "Boot." (and the OEM partition doesn't show up at all even though it shows up in Disk Management)

Clearly Clonezilla completely horked all this up.

I do believe at this point that the OEM partition is not the bootloader. It's gotta be the OS partition (in our case, volume 2). But nothing seems to be able to convince the system to change this.

We tried >bcdboot again to see if we could get it to mark volume 2 (OS) as the boot partition, but it won't.

????

here's something curious:
I tried setting the attributes of volume 1 (Recovery) to hidden, since that is how it shows on the correctly functioning computer. It did this, but then it likewise marked volume 2 (OS) as hidden.

So I selected volume 2 and cleared the hidden attribute, setting it to active, and then we are back to both volumes being unhidden.

Combine this with the fact that in list volume, volume 1, C drive, is the recovery partition. This should not be the main partition. OS should be. Volume 2 ought to be volume 1, C drive.

So should I be setting about making Volume 2 into C drive?
 
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More on this...

Here's what we've tried:
We reset the drive letters so that OS is C: and Recovery is D:--however, of course, we can't change the fact that D: RECOVERY is still Volume 1.

Upon attempting to restart, instead of "Bootmgr missing" we got "disk read error"

So we booted from the Win 7 disk, got to the command prompt and ran:
bootrec/ rebuildbcd

this scanned the drive and found windows on drive C. (The new volume C: OS, which is as it should be). We set this as the boot drive.

then we ran
bootrec/ fixmbr
and
bootrec/ fixboot

However, when checking the partition listing, it's still not listing C: as the boot partition, and on startup we still get disk read error.

Still working on this...
 
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OK, this worked to unhide the drive and then we ran bootrec again as above, which then set volume 4 as volume 1. But on attempting to reboot, we still got disk read error.
 
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I used the process you described above of setting the ids so that D: RECOVERY was set to id=27, and set the OEM volume back to hidden. Then when I ran bootrec it restored the volumes to the correct order as shown in our correctly functioning computer.

We then even ran >bcdboot c:\windows but I still can't get any of the volumes in diskpart to be listed as the boot, and attempting to boot still gives me a disk read error.

I think the answer here is that clonezilla completely horked up how this HDD is set up. It probably doesn't help that I've messed around resetting drive letters and whatnot.

Probably at this point I either need to start over with another attempt to clone using a different software (either EaseUS Todo Backup or AcronisTrueImage) or to start with a fresh install. 🙁

If you have any other ideas I'd be happy to hear them...
 
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Drive letters in recovery environment do not matter. They have no relation to drive letters, when you boot into windows.
Ok - one more option.
Delete and recreate 78MB partition.
  • diskpart
    list disk
    select disk 0
    list partition
    select partition 1 (make sure you select the right partition - 78MB)
    delete partition override
    create partition primary
    format fs=ntfs quick
    active
    assign letter=o
Then recreate bcd store
  • bcdboot d:\windows /s o:
d - volume letter of os partition, o - volume letter of bootloader partition
Then perform startup repair.
 
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