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Volume on spare drive marked as system partition

Volume on spare drive marked as system partition

I have an odd situation. I have 2 drives in my computer running Vista, the OS drive (C:, E:) and a storage drive (D:). In Disk Management the C: volume is listed as the boot partition and has all of the system files. The D: volume has the "System" flag, but (right now) there's absolutely nothing on it. I'm hesitant about pulling the drive or even repartitioning using a 3rd party tool (since Windows won't let me) as I've read that if a system volume isn't detected Windows can have a conniption. Any ideas?

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