Well not to be all smartass about it, i would for the next time you invest in servers, use 2$ extra and get a onboard raid solution, because as you plainly see software raid for the OS is not the smartest thing out there.
Im not very experienced in using software raid on OS drives. so i must admit i got no idea as to why it needs to switched over, i could imagine its something to do with the ID tags the boot.ini file uses, but it might even be a controller issue, that doesnt allow you to boot correctly without a drive in the correct SCA slot.
What kind of servers are you using?
This is a clear example of how companies often buy before they think (my company does the same, only in 100.000$ software solutions we allready have)... the amount of money the company have lost both to your workhours, and due to downtime.... hell you could prolly have replaced all the drives with sparkling new ones for that price