This guide is for UEFI-GPT Windows installs. Microsoft's bcdboot utility can recreate the bootloader on any selected partition quite easily, and it won't break any existing EFI entries (unlike the bootrec /fixmbr on MBR installs).
This process can be done on a working Windows install, or on the Windows Installer. To access the Command Promt on the Windows Installer, press ShiftF10 after the Windows Setup window appears, or click Next > Repair your computer.
You can do this with Disk Managment as well, if you can boot the installed Windows.
Enter diskpart
diskpart
Look at the volumes on your disk. You need to find the Windows volume and the EFI volume. The Windows volume has NTFS filesystem and is usually large in size. The EFI partition is usually between 100MB and 500MB and has FAT32 filesystem.
DISKPART> list volume
Volume ### Ltr Label Fs Type Size Status Info
---------- --- ----------- ----- ---------- ------- --------- --------
Volume 0 System Rese NTFS Partition 350 MB Healthy
Volume 1 C NTFS Partition 239 GB Healthy Boot
Volume 2 FAT32 Partition 500 MB Healthy
After you located the EFI volume you want to create the bootloader on, assign the letter S to that volume.
Use the appropriate volume number!
DISKPART> select volume 2
DISKPART> assign letter=S
Look at the volumes again, to make sure the desired partition got the S letter.
DISKPART> list volume
Exit diskpart.
DISKPART> exit
We are using the bcdboot utility. The first parameter is the Windows folder. The /s flag lets you specify the destination EFI drive.
If you are doing this from the Windows installer USB, the drive letter of the Windows drive will not be C:. Substitute the correct drive letter.
bcdboot C:\Windows /s S:
This creates the bootloader on the selected partition. You can reboot now, and the UEFI will hopefully find the Windows Boot Manager.