To fix the Windows Boot system using a command called 'BootRec' open a command prompt in administrator mode and type the following commands in listed order. After you type each command press enter.

bootrec /RebuildBcd
This will Scan all disks for installations compatible with windows and allow the users to choose which to add to the boot configuration store.

bootrec /FixMbr
Writes the Master boot record of the system partition using the master boot record compatible with windows. This operation does not overwrite the existing partition table.

bootrec /FixBoot
Writes a new boot sector onto the system partition using the boot sector compatible with windows.

bootrec /ScanOs
Scan all discs for installations compatible with windows and display the entries that are currently not in the boot configuration store.

Sometimes Win dows won'y know what type of boot manager to use. New systems like windows 10 user a boot managaer whereas older systems use NTLDR. To set either one of these in your system type one of the  following in your command prompt window and press enter..

For BOOTMGR
bootsect /nt60 sys

FOR NTLDR
change to /nt52