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If I were to remove a mirror during a Software RAID 1 re-sync on Windows Server 2012 Standard would it stop the re-sync and let one drive continue as normal, or would it break windows and crash the server?

The RAID is the boot drive, and it's this button that I'm talking about: http://prntscr.com/bzlbx1

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I don't know what will happen if you try to remove the array, but Microsoft says:

https://technet.microsoft.com/en-ca/library/cc787944(v=ws.10).aspx

Once you remove a mirror from a mirrored volume, the removed mirror becomes unallocated space and the remaining mirror becomes a simple volume that is no longer fault tolerant. All of the data on the removed mirror is deleted.

Besides, if you leave the disks in an inconsistent state, one disk will be different than the other (corrupt). Best to wait until they are synchronized before you do anything.

You are supposed to wait until the disks are consistent and then select Break Mirrored Volume to create two separate disks/volumes that are identical (because the disks are consistent!).

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