I cloned my existing 500 GB HDD to a new SanDisk 1 TB SSD (via CloneZilla).

Now, I'm having trouble to get Windows booting again:

  • SSD itself works fine, I can access it via Ubuntu (booted from USB)
  • the SSD is NOT recognized by the BIOS if I go into the BIOS setup menu
  • I then added a new partition to install Ubuntu as second OS on the disk, this works fine
  • The Ubunto Bot Loader (Grub) shows Windows 7 as an Option
  • When I Select this option, a flashing _ shows, similar to what is described in Windows 10 fails to boot after HDD clone to SSD
  • When I boot from the Windows 7 DVD and select recovery, my Windows gets detected
  • However, if I do "bootrec /RebuildBCD" or "bootrec /ScanOS" it does NOT find Windows Installations (!) i.e. it shows "0" installations found
  • I tried bootrec /fixMbr and bootrec /fixboot which did not help; also the automatic repair did not help

What is the difference between what bootrec is doing to find an installed windows (which does not work) and what the recovery and GRUB and others do that do find my Windows?

I still try to avoid to do a re-install of windows ...

  • If the SSD isn't found by the BIOS - First try a bios update, then try another SSD if possible. Aug 15, 2016 at 9:31
  • Ah, BIOS Update is an idea; however, the SSD works fine under Ubuntu - does Windows rely on BIOS and Linux does not?
    – Peter T.
    Aug 15, 2016 at 10:06
  • BIOS is relevant in both OS's - It should appear regardless, hence worth trying a bios update Aug 15, 2016 at 10:43
  • See my answer here and let me know if by change this helps you resolve the issue just in case: superuser.com/questions/1111110/… Aug 15, 2016 at 22:38
  • Thanks @PIMP_JUICE_IT for your hint. I just didn't have the time yet to give it another try to get it running. I did not try all of the things you mentioned. An I believe, it could be a problem with UEFI, since Linux works fine. What did surprise me is the fact that bootrec /rebuildbcd does _NOT _ find any suitable partition (while the Windows repair tools do finf it. Any idea what could be the cause?
    – Peter T.
    Aug 21, 2016 at 19:46

3 Answers 3


You can try to re clone the dd into the ssd on a linux live with the dd command:

dd if=/path/to/src of=/path/to/dest

Be sure, to unmount the dest partition before.


Finally, I ended up and deleted all partitions on the ssd, but the recovery particion and installed Windows 7 from scrath with the Windows setup creating new partitions. This time Windows 7 did start perfectly as expected and quite fast :-).

Then, I cloned my old Windows 7 partition again, but only this partition. This did the job.

No idea, what went wrong the first time. And I really don't understand why the output of bootrec /ScanOS differs depending on wether the Windows recovery was started from DVD or USB ... Anyway ...



Before we dive into the waters of that terrifying statement, lets eliminate some of the basics.

First of all, you shouldn't be trying to repair a cloned drive. If the source drive was in good working condition, the clone should come out the same. If the source drive was defective, that's a different story. To correct your problem you need to go back to the clone and get it right.

1. Make sure both your bios and SSD drive have updated firmware.
I know this sentence is annoying, but it may be the difference maker here. Most SSD manufacturers are releasing firmware updates to battle a huge plethora of issues and incompatibilities that are arising as SSD drives become mainstream. The firmware update will erase all your data, so it needs to be done pre-clone.

2. Try new SATA cables and ports
When I say this I don't mean to just plug the drive into a new cable and hope it boots, I mean do your clone again with new or different cables and switch up the ports. Motherboards often supply extra SATA ports with additional features, that may cause problems, or a particular port may be defective. If the SSD is your C: drive, it's good practice to have it on port 0 or 1.

3. Try erasing the drive and initializing it before you clone
When I say erasing, I don't mean formatting, you should do a sector by sector wipe of the drive. There are many freeware applications to perform this, such as Active KillDisk. Once this is done, initialize the disk to match the source drive, whether it be MBR or GPT, make sure it is the same. Now try your clone again. Hiren's Boot CD has everything you need for this.

4. Try different cloning software
I personally have had scenarios where one piece of software creates a drive that won't boot and another does a perfect clone, and vice versa with the same software. One would assume, that different software is using different methods of transfering/migrating the data. It also seems to be based on which particular SSD drive you are using. I personally prefer to use Acronis True Image 2015 (not free) for this type of stuff. You can erase the disk, initialize it, and clone, all in a bootable suite that supports SSDs.

5.Try your clone in a different PC
This one is self explanatory. Once the clone is done, put the drive back into the PC it's intended for. Cross your fingers as it attempts to boot into windows. You may have some luck after all!

If you have exhausted all these resources, you may have an SSD / mobo incompatiblilty and there are only two ways to solve that... The fact that yours is not recognized in the bios is a key indication that there may be a disagreement. One of the most common feuds is Sandforce controllers vs Nvidia chipsets. Do some research and see what you can find, keep in mind though that SSDs have just recently become common hardware, so you might not find exactly what you're looking for. The best way to be certain of this, is to contact your SSD manufacturer. They will be able to tell you if your ssd is compatible with the rest of your hardware. If it isn't, you should be able to sell it for near market value to someone with a compatible system.


You may be able to get around an incompatibility with a PCI-express sata card. Some people have had success with this. I'm not sure how stable it is or how it will effect read/write speeds, but it may be an affordable workaround.
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  • Thanks for your long answer. The SSD cannot be incompatible with my board, since it works fine with Ubuntu and I can access all my windows files from Ubuntu. It's only the Windows that does not boot. Could this be an UEFI issue? Maybe caused because I adjusted the size of the partions as the new drive is larger?
    – Peter T.
    Aug 21, 2016 at 19:48
  • I wouldn't be so certain. Have you used Ubuntu expensively with this drive? An incompatibility may only have subtle issues; freezing, hanging, file corruption. What brand and model is your mobo? Did you proceed through my list of suggestions? I have cloned many hard drives and those are the most common fixes to a bad clone.
    – Cosco Tech
    Aug 21, 2016 at 19:53
  • I'm not sure about uefi, but it's definately not from resizing the partitions.
    – Cosco Tech
    Aug 21, 2016 at 20:06

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