You replaced them how by the way?
I simply booted into linux, mounted the EFI partition (it's really just a fat32 partition, so any linux live cd or other linux system will mount it), then replaced the file with a mv command:
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mv EFI/ubuntu/grubx64.efi EFI/Boot/bootx64.efi
And why? To be able to select at run time the OS to boot?
Correct. I had Windows and Ubuntu installed, and the VM would always boot the bootx64.efi, which would boot right into Windows , without me being able to boot into Ubuntu instead.
So I replaced the Windows Boot loader with the grub loader to be able to select which one to boot.
why a dual boot VM and not two VMs?
Well, that's a longer story, and it will probably go a bit off topic. It really is not just a standard VM, otherwise you would be right - just have two and be done worrying.
I have a working laptop with LinuxMint running fine on a regular HDD. I just added an additional disk (SSD) to that laptop, which will in the future host both Windows and LinuxMint OS as dual boot.
However, just setting up and configuring both systems in "bare metal mode" so to speak, would have meant that my laptop would be unusable during all this time and I would not be able to do any real work on it.
So instead, I had set up this VM with raw disk access to the new SSD. Then I installed both OSes in the VM, which was pointing to the physical SSD, while I was still able to use the exising OS to do work as usual.
Plus, I was able to run the new LinuxMint OS in the VM inside the old OS and do a side-by-side comparison of behaviour and configurations if anything weird would have popped up.
Now that everything is done, I just boot the laptop into the new OS on the SSD.
The same way, in the new LinuxMint OS, I could now also set up a raw disk access VM for the new Windows or for the old LinuxMint on the first HDD (this one will remain in the machine).
The ultimate goal is to have the new LinuxMint and Windows OS on the SSD run in parallel at the same time, one as physically booted host OS, the other as VM guest via raw disk/partition access; being able to chose either one as host or guest at any time. And also, to have both of them behave the exact same way no matter if they are running as host or guest inside the VM.
So when I am working in LinuxMint, I can just quickly kick off my regular Windows OS inside the VM, rather than having to save everything, shut down Linux, boot Windows, do what I need in Windows and then reboot back into Linux. And even though it's a guest inside the VM it is still my "real" Windows environment, not a second Windows VM that lives in some vmdi...