Server 2008 R2 requires 2 disks to boot

The computer was booting off one of those disks you removed, and starting the OS from the Operating System disk (which is apparently a separate disk). This is what happens when someone carelessly installs an OS.

You need to get the BCD on the OS disk and corrected for it's new location. You may be able to boot the Installation Disk and Repair the installation into booting again.

Update - To Fix:

• First a backup: run bcdedit -export C:\bcd.backup, should probably copy this to another computer or thumbdrive.
• Open Drive Management, mount the boot partition (should be 100 or 300 MB) to a drive letter, note the letter.
• mkdir C:\boot
• xcopy /e x:\boot c:\boot (where x: is the drive you just mounted)
• bcdedit -export C:\boot\BCD

• bcdedit -store C:\boot\BCD -enum all
  Note the entry identifier and property of any lines where the second column says partition=x:

  For example:
  

  Windows Boot Loader
  -------------------
  identifier          {current}
  osdevice            partition=x:
  

• For each occurrence noted execute the following; be extremely careful to not screw this up!
  bcdedit -store c:\boot\BCD -set {current} osdevice partition=c:

  Note: change {current} to whatever the identifier of the section was for the property you're changing. Then just follow it with the property and new value. Also note the new c: value instead of x:. Also, the identifiers may/will be GUIDs.

• Once that looks all good, fire up Drive Management again, remove the drive letter from that other drive so it's back the way it was. Mark the C: partition Active.

You should now be able to remove the other disk and boot off the system partition. If this doesn't work you haven't messed up the other disk and can put it back in.

Update 2:
Looks like you've got that other partition mounted as h: already, so ignore that mount and unmount stuff, just jump into the copy, edit, yada yada.

If this is just a secondary DC (no such thing as a backup DC), why not just dcpromo it out, blow away the OS and start over?

First, a little history since it will make clear what is going on.

In the past with Server 2003 and before for NT-based OS'es (not the 9x OS'es), you had a boot.ini, which had a line similar to this: default=multi(0)disk(0)rdisk(0)partition(1)\WINDOWS . This told the NT loader where to find the OS to boot from.

So if you had a boot.ini that booted from partition(2), but you remove partition(1) because it is on a different disk (or even change the boot order of your disks in the BIOS), when you boot, it is still looking for partition(2), but it has, in effect, been moved and renamed partition(1) so it won't boot since the required files are not in that location. The same goes for changing of disk numbers.

In Server 2008, the boot.ini has been replaced with the BCD (Boot configuration data), and needs to be edited using the BCDEdit tool. Here is a good tutorial on how to use it: http://www.computerperformance.co.uk/Longhorn/server_2008_bcdedit.htm

When you removed that disk, you changed your partitions and/or disks, and your server is not looking at the right partition/disk to boot from. When you fix the boot configuration data to look at the right disk and partition, it will boot.

Windows 2008 R2 (every Windows since Vista, actually) has taken the Linux approach of separating the boot loader from the operating system, by storing it in a separate partition; if you take an empty disk and tell the Windows setup to create a single big partition in it and install Windows there, it will automatically create a small (~100 MB) partition at the beginning of the drive to hold the boot manager, and then it will actually install Windows in a second partition filling the rest of the disk. This will happen automatically, and you can't even avoid it: Windows can have the boot manager and the operating system on the same disk, but the only way to achieve this is to install it in a disk which has already been partitioned.

Ok, this was a little digression; anyway, looks like in your case the partition holding the boot manager somewhat ended up on a different drive than the one holding the operating system; but we don't know the actual disk layout from your question: we only know the boot manager is stored on H: and the O.S. is on C:, and from your description of the problem, looks like H: resides on the disk you were trying to remove.

You should post some output from the diskpart command, or, even better, a screenshot from the Disk Management snap-in.

As for moving the boot manager, yes, that can be done, but it's somewhat tricky, so please post more informations about your actual disk layout before we can provide you with a solution.