Boot from Windows media (Windows 7, 8, 10).
Select the correct time and keyboard type (or just continue).
Click Repair your computer in the lower left corner.
Select Troubleshoot from Choose an option screen.
Click Advanced options in Troubleshoot screen.
Select Command Prompt.

Use the following commands to diagnose and fix BCD store related errors:
bootrec /fixmbr
bootrec /fixboot
bootrec /scanos
bootrec /rebuildbcd

If you are deploying WIM images via a WinPE command shell you can use the following command to configure the BCD store for first use manually:

C:\Windows\system32\bcdboot C:\Windows /s S: /f ALL

Where [C:] is the volume holding the Windows installation (System partition) and [S:] is the volume containing the EFI folder (Reserved partition).  You can use diskpart ‘list volume’, ‘select volume’ and ‘assign letter=’ to set the correct drive letter for the correct partition.