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Intel RAID5 Problems

I recently did some upgrades and installed a new copy of Server 2012 R2 on a new 2TB RAID5 Array.

Everything seemed to go fine and its been running for a few days but I guess I wasn't paying close enough attention because I just went to tear down the old RAID1 array and apparently the system reserved vol from the new 2012 install ended up on the old RAID1.

Luckily I was able to recover the server by reinstalling the disks.
I have a copy EASUS Server edition that I can use to copy the system volume over to the new array but will it work?
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Stampel

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It didnt work. After reboot- the system, protected drive is still the old one.
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Stampel

I dont really understand. Cant you just backup your data, keep only 1 RAID and restore on this one.
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So is it booting the old system, or the new one. Is it giving you a choice of where to boot from?

If its just booting the old drive, can't you just pop out the drives the old system is on and it will now find the new system installed on the new drives.
No Boot Choice. Somehow booting windows from intended raid but using system drive from old. Very strange!  I do however only have hyper-v and updatesd installed. It would take several hours but I could reinstall if necessary
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Worked like a charm. Why do they not offer advanced options for S2012 R2 Repair like they do with W8?
Everyone helpful but link I posted is the solution. Occasionally the system drive install on other partition and/or Windows install binds to existing system drive.