To rebuild the BCD or Boot Configuration Data file in Windows 10/8/7, in an elevated Command Prompt, type the following command and hit Enter:

bootrec /rebuildbcd
This will scan for other operating systems and lets you select the OS’s you want to add to BCD.

BCD or Boot Configuration Data is a firmware-independent database file which has boot-time configuration data. It is required by Windows Boot Manager and replaces the boot.ini that was used by NTLDR earlier. In the case of boot problems, you may be required to rebuild this file.

If this does not help, you can try this - but do so only if you are an expert, as it could create issues.

In the elevated command prompt, type the following command and hit Enter:

bcdboot c:\windows /s c:
This will give you a new Bootloader. Here "c" is the system drive.

You can get the explanations on BCDboot Command-Line Options here on Technet.

You can also use EasyBCD or Dual-Boot Repair to repair your BCD file. It also lets you repair & rebuild MBR.