Hard Drive Bay 2 Doesn't Show Up, RAID degraded.

I'm getting ready to do a major application upgrade to an existing Xserve (Early 2009). I've noticed that the Bay 2 Hard Drive wasn't showing up in the RAID Utility. I got a spare drive and tonight I powered down the server, swapped that drive out and brought it back up. The system is running fine, but it doesn't seem to recognize the drive in the bay. Either in the System Profiler or in the RAID Utility. I've tried both the old drive and a brand new drive that's meant to be an Apple Xserve replacement SATA drive. I'm concerned that this bay has failed, and if so, I need to sort out what part that is to be replaced. We bought a repair kit when we both he server, so I have a number of parts for it, including a system board.
The Xserve (Early 2009) is running Server 10.6.8, serves up files from an attached Promise VTrack E-Class drive array. I'm getting ready to upgrade from Server 10.6.8 to 10.9.5, which I guess is a 2-step process, (upgrading from Server 10.6.8 to Desktop 10.9.5 then putting Server 3.x on top of that.)
If there's some insight into this issue or if the HD Bays are connected to the system board or something else, that would be wonderful to hear.
Thanks in advance!
--Michael

You could try the xserve in target disk mode connect it to another mac and try swapping the drives, drive bays around to try and pin point where the problem is

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Hard Drive Bay 2 Doesn't Show Up, RAID degraded.

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