Can’t boot to SCSI after killing CMOS

I had to use killcmos utility on a server that someone had set a password and left without informing anyone of the password. I had intended to format the HD’s and start over, but now Winnt 4.0 server won’t install. It acts as if it is going to work (format, initial setup files, seem to work) but when the system reboots, it gives a missing os error. It seems that I have lost some space due to the scsi misreporting one of my drives. How can I get this back to a place where everything works okagain???!!