boot - Repair BCD for a Windows Installer on Grub2 Portable Hard Drive

I have created a external hard drive contain GRUB2. This drive can boot the following:

• Windows 10 PE


• Ubuntu 16


• Many ISO files.

Now I want to include Windows installations. My problem is I want to put each version of windows in its own folder like so:

• DIR windows10x64


• DIR windows10x32


• DIR windows8x64


• DIR windows8x32


• DIR windows7x64



• DIR windows7x32

The issue now becomes that moving the installation files from their root directory to these folders messes up the BCD. I know you can use bcdboot to repair the BCD in a windows file system. My issue is there is no windows file system within the install files.

Is there anyway to repair the BCD on a windows installation USB?

Thanks!