It seems we have several different issues here:
2. Missing VD. May need more information on your RAID configuration. What do you see in RAID Web Console 2? Do you still see the physical drives?
3. BMC failed. This doesn't look good... Did you try to unplug the power cord from the system to reset the BMC? Can you try a BMC firmware update and see if there is any errors?
Yes, I thought it was a corrupted BMC. Tried forced update etc - nothing worked. Replaced with Advanced replacement. Already installed and it works perfectly.
In regards to the RAID issue.
Yes, I'm aware that new drive become a hot spare and Intel Embended RAID doesn't support JBOD.
The issue was that after disconnecting hot spare virtual drive became unreadable. Though, I could still see it as the Virtual Drive with two physical discs, I could access the info on it. After disconnecting both of the physical drives from the system, I couldn't find ANYTHING on both drives.