Error reading boot configuration data on primary hard drive Windows Web Server 2008 R2

I have a root server on Hetzner which is running Windows Web Server 2008 R2. I am facing an issue with boot up. The server hangs up for some reason and when I issue an automated restart from Hetzner's control panel it doesn't boot. I got the KVM access and saw the boot up was failing with status message 0xc000000f, "An error occurred while attempting to read the boot configuration data."

Upon continuing I saw two operating systems listed - Win Server 2008 and Win Server 2009 Secondary Plex which I believe is on the mirrored hard drive I have, I am able to boot up using the secondary plex option. However If I have to restart the server I again face the same issue. So I can't reboot the server without asking for KVM access every time.

I asked Hetzner to attach a Windows RE USB stick which they provided promptly but when I tried to repair using the disk I got the message

"This version of System Recovery Options is not compatible with the version of windows you are trying to repair. Try using a recovery disc that is compatible with this version of windows."

I contacted Hetzner and they were able to boot into the recovery mode however it did not list any Operating systems to repair. Hetzner also ran a check on hard disks and concluded the disks were fine. SMART status check on disks is also showing all OK.

It seems the boot record on primary disk has been corrupted somehow so I have to boot from the mirrored disk. It seems the boot configuration on the mirrored hard drive is OK.

How do I fix the boot record on the primary drive? Any help would be appreciated.