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Break and re-start software mirroring

I'm running Server 2012 x64 and was using software raid to mirror two PCI-e SSDs.  However, I've found that the backup card is not actually mirroring the primary; if you boot from the secondary card, the system boots as it was on the second day of use.

If I try and delete the volume on the secondary card and re-do mirroring, Windows tells me that I can't delete a system partition.

How do I make the mirroring start working again?
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Venugopal N
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Have both the disk on the system and login to the 2012 server ( as normally it will login with the use of primary disk) and from disk management.Select the disk and right click and click break the mirror.Restart and now try to delete the partitions on the secondary drive and try to create the mirror.
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As you brake the mirror and try to delete partition see if this partition is marked as system boot. If yes then your are booted from this partition.
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Venurajav -  I don't have that option...everything is grayed out.

noxcho - It is marked as a system partition.  I did some more digging yesterday and for whatever reason, we're running off the secondary card, which made Windows create the system partition on Disk0.

The plan to fix this is:  Run VMWare Converter to move everything to a VM (as a backup) and run some disk part tools to move the system partition to where it's supposed to be.  Has anyone done this before?
Actually you can try to change the drive order in BIOS. Swap the order of disks 0 and 1 and then see how it detects the drive.
Also, can you please take a screen shot of Windows Disk Management and post it here?
You mean swap the order of the boot disks?  I don't see how that will work, as the system will try and boot from the other disk, which wouldn't work because it's an out of date image.

Screen shot attached
Interesting, at this time your system is using Windows folder from disk1. And booting from disk0.
Yes, swap the order and see if it starts using files from single disk. Not from two.
But, that's now how the BIOS sees the drives.  According to DiskPart, I'm actually running off Disk1, not Disk0.  I've read that Windows always names the drive it's running on as 0 and increments from there.

I'll be running the VMWare Converter this weekend and will be able to play with the server more next week (it's in production now)
your image suggests you don't have a mirror set up to break in the first place.

just right click your active drive and select 'add mirror' then choose the other disk and away you go!
Can't do that, see original post
dammit. apologies. couldn't see it properly on my mobile!

Yes, it looks like the 2nd disk as been setup as your 'system' volume and is therefore in use.

As this means it is used to boot your system I'm afraid you are a bit stuck. You cannot wipe, swap or change either of the disks because it will prevent your system from booting.

Converting to a VM is an option but you'll have to convert BOTH disks to your VM to ensure it works.
If you were planning to restore it to this server after sorting the mirror it wont work as you wont have 2 separate disks to restore to.
If you change the disk order this could do the trick. Try that you can always revert it back.
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