MSR partition contains boot files for Windows to boot and if this partition is lost, Windows will not boot.

The solution is to recreate boot files on System Partition. 

Problems

When MSR (Microsoft Reserved) partition is lost on Windows 7 / Server 2008 R2, Windows will fail to boot

Solutions

 Recreate BCD on System partition using Windows Setup DVD

 Steps:

1. Boot Windows Setup DVD (Windows 7 / Server 2008 R2)

 2. Press Shift + F10 to open Command Console

1. To recreate BCD boot, the partition must be set to active. Run Diskpart command to set active

X:\sources>Diskpart
DISKPART> List Disk
DISKPART> Sel Disk 0
DISKPART> List Par
DISKPART> Select Par 1
DISKPART> Active
DISKPART> Exit

1. Run BCDBoot command to create Boot files

BCDBoot C:\Windows

Note: If there is an error when running BCDBoot, you need to set the partition to active first (refer to item 3)