Yep. Your Windows 2008 R2 server wont boot. This is quite common if you mistakenly make your C: partition active when no bootmgr is on this volume.
Steps to fix are:
1) Insert Windows 2008 disk and boot from DVD/CD drive.
2) Follow the Install guide -> Select the Repair option -> Click Next
3) Choose the Command prompt and input the following commands:
List the drives on this machine
Select the C:/ drive (normally disk 0)
select disk 0
List the partitions on the C:/ drive
When the partitions are listed look for a ~100MB partition – usually partition #1
select partition 1
Activate the partition
That should do the job.