How to fix Windows 2008 R2 BOOTMGR is missing

BOOTMGR IS MISSING
PRESS CTRL+ALT+DEL TO RESTART

Note: This is a VM on VMWare ESX server, but that should not matter

I put in the 2008 R2 x64 install dvd and can get to recovery, but it lists no Operating Systems. Clicking on Next brings me to

+===========================
System Recovery Options
+===========================
Choose a recovery tool
Operating system: Unknown or (Unknown) Local Disk
.....

Command Prompt

I start the command prompt, go to C:\ and perform a dir /a

Apart from files I put there myself, these are showing

$Recycle.Bin
Documents and Settings [C:\Users]
Program Files
Program Files (x86)
ProgramData
Recovery
System Volume Information
Temp
Users
Windows

Where to go next? Is it like the NTLDR problem with Windows 2003 where I can just drop a file in there and it will be hunky dory again?


Try BCDBoot.

Boot from the windows CD then go to the command prompt.

Type

BCDBoot c:\Windows

I have had an immense amount of trouble getting windows to boot on a new 1TB disk. It booted off the new drive so long as the old drive was plugged in to the first SATA port, but after a year of running like that the old drive finally died.

I followed the advice of @SLY and @JFB and also this useful hint on how to access the Startup Repair function under Windows 2008 R2 Server from the command line. (x:\sources\recovery\StartRep.exe)

After much trial and error I did get this machine to boot with only the new drive connected, so I can finally pull the aging OEM drive. As I don't really know exactly which step fixed it, I am just listing what I did below.

; Initial condition: will not boot, says "NTLDR IS MISSING". 
; Booting off Win2k8r2 install CD. In recovery window, no windows installations appear.
; From command line, partition is present and seems ok.

BCDBoot C:\Windows 

; after this step the windows 2k8r2 installation appears. Still fails on reboot.

Bootrec /rebuildbcd

; after this step it found an installation and allowed me to select it. Fails on reboot.

x:\sources\recovery\StartRep.exe

; startup recovery runs, claims to fix some stuff. Fails on reboot.

bootrec /fixmbr
bootrec /fixboot
bootrec /rebuildbcd
x:\sources\recovery\StartRep.exe

; One of these four commands fixed it. This time bootrec /rebuildbcd 
; did not find any orphaned installations, and StartRep.exe said that
; everything was fine.
; Rebooted one more time and it worked.