Windows won't boot without secondary hard drive. Repair or reinstall?

[Brodieman]

Hello all.

The current configuration of my PC is two 320GB WD drives, main drive C: and secondary S:. Recently I began to experience disk read errors when attempting to boot, and a battery of tests revealed that drive S: is on the brink of failure. Fortunately (or so I thought), scans and SMART reports on C: are clean, but I figured this was a good time to upgrade to a 1TB main drive and retire C: as the new storage drive as it's fairly old.

I was hoping to clone C: over to the new drive to save me the trouble of installing 300GB worth of applications and losing all my settings, etc. However, when I attempt to boot with C: and the new drive, I receive a "no boot device available" message. bootrec /ScanOS in Windows 7 repair mode finds the installation of Windows 7 just fine, and I can browse the boot sector in recovery mode as well. There shouldn't be a problem.

I found these two recent threads that address a similar problem: http://www.tomshardware.com/answers/id-2583303/boot-secondary-hard-drive-plugged.html
http://www.tomshardware.com/answers/id-2221990/installed-windows-drive-drive-storage-windows-wont-boot-plugged.html

It seems that Win7 was installed with both hard drives plugged in, and now C: can't live without S:

In both cases, the solution presented was to do a clean install of Windows. Since I was hoping to clone C: to the new drive, is it possible to just repair the Windows installation with the setup disc to make it independent of the secondary drive? Alternatively, can I reinstall WIndows, without S: this time, and still retain all my programs and data?

 

[ArtPog]

Setting aside your 1 TB HDD that was the recipient of the clone...

If you boot to the 320 GB HDD that contains the Win 7 OS and that drive is the ONLY drive connected in the system at that time...
Does the drive boot without any problem and does it then function problem-free?

Why don't you respond to the above and we can go on from there if you want.

 

[SBMfromLA]

I know exactly what your problem is... Your boot loader is located on the drive you want to remove... that happened when you installed Windows with two hard drives active in the computer... For example.. If you originally had Windows installed on a hard drive... then at a later point in time you installed a new hard drive and then installed Windows onto that new hard drive... The boot info that was originally written too the first hard drive does NOT get deleted... it gets appended with the new Windows install.. so even installing a new hard drive... the other hard drive has the boot information.. That is why it's recommended to UNPLUG all other hard drives when you install Windows... so the new boot info gets written to the new drive instead of being appended on the older hard drive...

The solution is simple..

Just unplug the other drives and boot from your Windows DVD... and get to the screen where is asks if you want to Repair the Windows Installation... You may have to run it up 4 times since it repairs in segments... but it will fix your problem.