What has happened is after the update, your BIOS has likely returned to the defaulted settings. The default settings do not include RAID support, and the controller will be turned off, or set for normal SATA operation.
You will need to set everything back to the original RAID settings.
Enter the RAID BIOS, and put the drives back into RAID 1.
If you have not done much, the controller should simply re-establish the array.
If you have been running with only 1 disk for a period of time, you may have to rebuild the array.
I think the only thing I did was defrag the drives. If I have to rebuild the array I will lose the info on the drives right?