When the Windows boot sector is corrupted or it contains invalid code for the version of Windows on the partition, it must be repaired, otherwise you will meet “BOOTMGR is missing” errors. Since the Windows installer updates the boot sector of the system partition during installation, this problem usually occurs when the Windows booting files are relocated from the install partition to an alternate partition or when installing an older version of  Windows on a system with a newer version already installed.

A solution to get rid of a damaged partition boot sector is to overwrite it with a new one using the bootrec command.

How to replace the damaged boot sector with a new one:

1. Start Advanced Startup Options in Windows 8 by typing “shutdown /r /o” in Start > Run or System Recovery Options in Windows 7 & Vista, for this reboot your computer, and keep pressing F8 key till a menu appears, using keyboard choose Directory Services Restore Mode.

2. Open Command Prompt, type “bootrec /fixboot” and press Enter. This command will write a new partition boot sector to the current system partition.

3. If you see the message: “The operation completed successfully.” with a blinking cursor at the prompt. This means the operation finished. Restart computer.

If the partition boot sector was the only problem, Windows should start normally now.

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