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Backupper breaks original OS when restoring to other location

When I restore my OS image to another drive, everything looks OK and whole process ends without errors. So I have 2 Windows installs on 2 different drives now.

After I restart my PC, this is what happens:

The original windows install, which was used to restore to another drive, start reading system files (mostly system dlls) from the other drive!

For example instead of reading from "C:\Windows\System32\some.dll"
the system process reads all dlls from "F:\Windows\System32\some.dll", which is the new install that I created via Backupper's system restore.

If I physically disconnect the new drive (F:) and restart PC, Windows read everything normally from C:.
If I reconnect the drive again the problem is back.
If I plug the drive to different SATA port, it fixes the issue and Windows will only read from C:.
If I plug the drive back to the original port, which was used during restore, the issue is back.

TLDR: After restoring OS to another drive, system process reads system files from wrong drive. The only fix is to physically plug the other drive to different SATA port.

Is there any way how to fix this? It seems to me that Backupper updates some system info, which confuses the system to prioritize the other drive to use for system files. I want to have both OSes in my PC so removing one of the drives is not an option.

OS: Windows 10 21H1

Thanks for any help.


  • @H8ts, When you connect the two disks, please try to boot computer into BIOS and then set the boot order again and then boot. And, please check if there are two "Windows Boot Manager".
  • Hello,

    boot order in BIOS is OK and also unrelated to this issue, because I change OSes via F8 during boot. They are on 2 separate MBR disks, both disks have "System Reserved" ACTIVE boot partition and Windows partition.

    And as I wrote before, the process reading from the wrong disk is just system process "PID 4". Other services for example read from correct disk. So basically that one OS, which was used during restore process, reads from BOTH DISKs now. Where the system process (PID 4) reads from wrong one and other processes read from the correct one.

    I can clearly imagine that this would lead to BSODs if those OSes weren't the same.

    Thanks for help!
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