Running two bootable drives makes one permanently unbootable?

Newmaven

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I am just finishing a clean reinstall of EVERYTHING onto a new drive. I had hoped, once I'd installed Win 7 Pro x64 in the new drive, I'd be able to put the other drive back in the system to transfer certain files. But every time I did, it rendered the new drive unbootable, even after I'd taken the old one out again. I'd still like to be able to transfer files directly between them -- is there any way I can?
 

My Computer My Computer

Computer type
PC/Desktop
Computer Manufacturer/Model Number
Dell T3400 Workstation
OS
win7 Pro x64
CPU
Intel Core 2 QUAD q6700 @ 2.6 GHz
Motherboard
Dell 0TP412.A02
Memory
8 GB, DDR2
Graphics Card(s)
nVidia Quadro NVS 290
Sound Card
motherboard
Monitor(s) Displays
Samsung T260HD and ViewSonic VA2702w
Screen Resolution
1920*1200, 1920x1080
Hard Drives
Seagate hybrid C:, two WD data drives. 5TB total
PSU
375W
Case
Stock
Cooling
air
Keyboard
Dell
Mouse
Logitech Performance MX
Antivirus
Malwarebytes, Norton 360
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IE 11, Seamonkey, Firefox, Opera
The boot partition on the old drive is likely marked as active. If you have a docking station or usb enclosure you could plug into a usb port then use Disk Management to remove the attribute.

Apparently diskpart command can do it:
http://www.sevenforums.com/hardware-devices/232286-remove-activeportion-harddrive.html

Just be careful when you select the disk to put the right number or you can hose the system disk.
When you do list disk
it shows all the disks on the system.. just be sure to get the right one.when you select disk.
 

My Computer My Computer

Computer Manufacturer/Model Number
HP Media Center
OS
Windows 7 32 bit
CPU
AMD 5200+ dual core
Memory
2 GB
Graphics Card(s)
NVidia GeForce 6150SE 128 MB
Monitor(s) Displays
CRT
Screen Resolution
1280x1024
Hard Drives
500 GB Sata internal :

SIIG USB 3.0 docking stations w/WD Caviar Black 6 Gb/s drives
Keyboard
PS/2
Mouse
PS/2 Wheel Mouse
Other Info
SIIG USB 3.0 PCIexpress card.
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