I recently updated my bios and upon restarting I discovered my Raid array was broken. I didn't manage to find out online how to fix it,  so I decided to describe the solution for other people in the same predicament. The problem arises when you have 2 discs in Raid and one without.

The first thing I tried to do was to change in the bios the storage configuration from IDE to Raid. This helped as the bios saw my raid but the computer wouldn't boot. It was recommended I try to downgrade the bios. I didn't think that would help but still tried. This wasn't easy as it is not always allowed with the regular bios update software (Asus board - some bios downgrading is allowed and some isn't and because of overclocking I cared about the particular bios). The solution for it I found was:
1. To download the HP USB disk storage format tool (http://files.extremeoverclocking.com/file.php?f=197) and make a usb stick bootable. This is a useful thing to have anyway.
2. Use the Afudos software (again, for an Asus board), but also here you need to find an engineering version as otherwise it won't always let you downgrade.

Downgrading predictably didn't help.

The solution turned out to be extremely simple. What one needed to do was change the order of the hard drives when they were in IDE so the correct one will boot. This sounds simple but whenever you change them and then move to raid the list disappears so it requires multiple reboots, and moving back and forth from raid to ide, until you get the correct configuration. (This was actually the first thing I tried, but I didn't fall on the correct configuration until I knew that this is what I had to do and play with it until I got it). You would think you could simply change the order of booting when in Raid and not IDE, but that didn't work even when verified later. (If your hard drives are different this becomes much simpler obviously).
FYI.