Today I updated the BIOS from version 35 to 48 then to 99 then to the current 117 BIOS in hopes of upgrading my CPU to a newer sandy bridge core I7. Before putting in the procesor I booted into WHS 2011 only to realize my raid array was no longer showing. Upon inspect my adaptec 6905 raid card is no longer being recognized by the motherboard even though it has not moved from the PCIx x16 slot that it was working in prior. The BIOS does not see it nor does the Raid BIOS come up. I have disabled UEFI and Trusted Boot as well as played with the video options to no avail. I know the card works fine as all the green lights come on. The card was working fine right up to the BIOS update. Unfortunately I cannot roll back the BIOS updates so any help would be appreciated. I have all my backups and data on that raid array.
In your case, I recommend accessing the BIOS and setting the BIOS chipset mode as RAID since after the BIOS update all settings will be reseted as default.
Per above it's not the onboard Raid I am using. I have an Adaptec 6905 Raid card installed in the PCIe x16 slot and with the BIOS update it is no longer recognized by the BIOS. It shows the slot as being empty even though the card has power and works fine.
In your case, I recommend you doing the following steps:
If issue persists, I recommend you doing a BIOS roll back to the previous BIOS version. You can check more information about the BIOS recovery process at the following link:
1. I already cleared the CMOS and removed the battery as well.
2. Drivers are updated however this is irrelevant since the raid BIOS does not come up upon cold boot
3. Motherboard does not see Raid card anymore but the BIOS is updated.
I cannot roll back BIOS as the updated BIOS for Windows 8 does not allow roll back. Please see if a BIOS fix is forthcoming for this issue.