Can not boot with second HDD disconnected

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memory

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Whenever I disconnect the storage drive, Windows will not boot. After doing some searching, I found out why.

Under disk management, the Windows drive is listed as boot, page file, crash dump, primary partition.

The storage drive is listed as system, active, primary partition.

This is the reason it will not boot with the storage drive disconnected, right? The Windows drive should be listed as system and active. I know I need the mark the Windows partition as active to fix this but will doing so affect the data on the storage drive?

When I first installed Windows, I had both drives hooked up. I did not realize this would happen. I am about to reinstall Windows and I want to disconnect the second hard drive so this will not happen again.
 
I did install Vista/7 several times with several other drives on. Might have to move off the paging on that drive.
 
I got it fixed.

I made the Windows partition active but that did not solve anything. I still couldn't boot with the second drive disconnected.

So I did a repair install with the second drive disconnected and that fixed the problem. I can now boot with the second drive disconnected.

I am about to reinstall Windows 7. Well before I did, I decided to enable AHCI in the bios. I was not expecting it to boot but it did, a little slow but still booted. Now it seems like I have more free space on the Windows drive. Before I enabled AHCI, I had 416gb free(I think, didn't really pay close attention to that number). Now I have 425gb free. Is that normal to gain free space by enabling AHCI?
 
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