Strange boot issue - Windows 7 - If I remove 2nd harddrive, windows wont boot

I have a 2nd harddrive that is starting to fail (data storage only drive), and when I replaced it with a new 1TB drive,
I got an error message and Windows 7 wouldnt boot until I put the 2nd drive in again.

Both the old and new secondary drives are completely empty (however in Disk Manager I can see the old secondary drive is missing 1 mb, so there must be some boot files there).

I have used Paragon Disk Manager before, but completely uninstalled it. But there must be some lingering boot files/data on the secondary harddrive (even though appears to be completely empty).

I have checked bcdedit and msconfig and Advanced System Settings --> Startup and Recovery --> Settings and looks like everything is booting from the C:\ drive.

How can I fix this and put back all boot related files only to the C: drive?

Thank you,
TheGreatEye OfSauronAsked:
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MikeIT ManagerCommented:
Have you tried running fixmbr from the recovery console?

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Your issue is that the drive you removed altered the reference to your drive and possibly a reference is missing.
Did you clone the new drive from the old drive? Often drives come with vendor CD to migrate the data from the old onto the new.
An option when the system is booting is to try to opt for the boot option (escape, F12, etc)
When prompted hopefully you can differentiate between the OS drive and the data drive I.e. One is 320GB and the other is 1TB and within the boot menu, you can differentiate, I.e, one if both are from the same manufacturer it might be ..... Differentiated, pick the one with the OS and see if you can boot from it.

Did you alter the cabling? I.e. Switching the drives positions?

You need to reconstruct the boot record using bootrec/bcdedit.

When you boot with the second drive in place look at diskmgmt.msc to see how is the second drive listed, does it have any system, boot, page file reference?
is windows set to show hiden files and folders?
probably you have the system partition (100-200 Mb) on the second drive
if you copy that partition to the other drive with a partition manager - it should boot again
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With the paragon disk manager make sure your OS disk is set to "Active". Currently your other disk probably is the active disk. Things like that happen if you install an OS with both disks there. I always recommend to remove all unneeded disks before installing an OS.
To fix it, first create a system repair disk:

Then disconnect the 2nd drive, and boot to the repair disk, and do a Startup Repair:

With only the main system drive connected, Startup Repair should reconfigure BCD and place any needed boot files onto the main drive.
TheGreatEye OfSauronAuthor Commented:
Excellent. I shall try this tonight.

TheGreatEye OfSauronAuthor Commented:
Interestingly enough, last night when I took out the second drive, it booted up fine. Which then allowed me to power down and add the
second drive.

I am sure the Recovery Console, Fixmbr and using the system repair disk would have worked.

Thank you all.
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Windows 7

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