Windows 7, Intel Software RAID, Boot BCD Error

 I had setup a computer about 10 years ago for a medical research study.  It was done for a specific piece of software.  It was setup with a NVidia 660, i5 2500, 12GB of RAM and 2 x 1TB Drives in a software RAID 1.  I've had to go in twice before, once to replace a failed drive, and to reset the administrator password.  This time I got a call because the system would not boot.  The issue was described to me that when the computer tried to boot into windows it blue screened and immediately reboot.  I made an onsite visit to inspect the system and did see the issue.  So I started the investigation by looking at the BIOS, sata settings and discovered it had been set to AHCI.

Once I changed the SATA mode back to RAID, the system still refused to boot, Windows recommended booting off the install disk and running a repair.  So I booted into the disk and ran the startup repair.  

As shown above we see the boot dvd sees the Windows disk, and detected an issue with the BCD file, but when you go to run the repair after a few minutes the recovery system says it failed to repair the BCD file.

Even after running a disk and file system check; the issue remained and the system was still unbootable.  What I eventually did was break the software raid; after doing that, and leaving one disk offline, the system booted.  After the system booted, I shut the system down and reconnected the mirror drive.  The system continued to boot properly and started to rebuild the software raid.