Asus Deluxe P6T V2 - Raid 1 Broken

When I originally installed my system (Windows 7 64 Bit) I had to 1TB disk drives mirrored (Raid 1) and could only see one volume (Drive C . It's been that way for a couple years. I just noticed the other day that I now have two drives (C: and D  and Drive D: has the same directory/file structure as C: but is not mirroring any more. BIOS looks to have set the SATA as IDE. The only way I can see this happeing was due to a BIOS upgrade I did a while back.

1) Does a BIOS upgrade by default reset the SATA RAID setting back to IDE?
2) If I try to re-enable the RAID setting in BIOS and through the Intel controller (CTRL - I) the system will not boot. Is the only option to re-enable to have to re-install the OS?