To re-create the boot partition follow these steps (taken from this article: https://blog.workinghardinit.work/2016/09/08/disk2vhd-on-a-generation-2-vm-results-in-an-unbootable-vhdx/)
A) Boot the VM to WinPE on the Windows Media - You'll need to create a DVD object in your VM by selecting the SCSI controller in the VM settings and adding a new DVD Drive, then either attach the .ISO or the physical drive with your boot media to that. Once this is done you can boot the VM, hit a key when prompted to boot to the DVD.
B) Go to a Command Prompt Once you have the Language window up, hit Shift-F10, or click Next, then 'Repair My Computer', then 'Troubleshoot', 'Advanced', and 'Command Prompt'. Both will get you to a Command Prompt.
C) Open Diskpart tool (careful in here...) At the command prompt, type "Diskpart" and hit Enter
D) Run Diskpart Commands:
List Disk (This will show you the drives, most likely there is only one, but either way, you need to select the boot drive with the next command)
Select Disk 0 (If you have multiple drives, this could be a different disk - you want the boot drive)
List Vol (this will list the volumes in the same manner as List Disk did the discs) Here, you should see your volumes, but your actual boot volume (not your System Volume, just where your Boot Configuration sits) will show up as "RAW". Note the Volume Number of this RAW volume.
Select Vol 3 (this is assuming that RAW Volume is 3 - use your actual Raw volume number)
assign letter L: (This makes the volume visible with a drive letter - we are using L: - this is temporary and only really matters during this Boot session)
FORMAT FS=FAT32 LABEL=”BOOT” (This will format the Volume and ready it to receive a new Boot Partition. It also names the volume "BOOT")
Exit (This gets you out of Diskpart)
E) Switch to Boot Volume and Create the Boot Folder Structure with these commands
L:
md L:\efi
md L:\efi\Microsoft
md L:\efi\Microsoft\Boot
F) Create Bootrecord and Boot Files with these commands
bootrec /fixboot
The end all Be all, recreate EFI partitions in disk genius:
Assign letter to fat32 partition, in this example L:
bcdboot C:\Windows /l en-us /s L: /f ALL
This creates the BCD store & copies the boot files from the windows system directory. (yes, that is "/L" indicating 'locale' - I am in the US, - choose your own locale)
At this point, you can exit the command prompt and restart the VM to the Operating System on the disk.