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The script just looks at how it was booted assuming the hd boot type would match. This is so it supports both efi and legacy bios from a single image. It doesn't need to match the original upload. At least I was working towards that, never actually been tested.
It looks like there is a flag to force EFI, you can try it out.
bcdboot c:\Windows /s q: /f UEFI
I don't think this will work. I believe it needs to be pxe booted in the same mode that it will boot from later. Basically the system partition and efi boot entries(nvram) are all created from a single command.
bcdboot c:\Windows /s q:
I think that Windows is detecting the system is not currently in EFI mode and doesn't run the necessary efi process. That is why the system and reserve are not imaged, they don't need to be because bcdboot takes care of setting them up. I think your only options are to boot EFI with USB/ISO, or change the system to always use legacy bios.
Please attach the upload log for the image and one of the failed deployment logs
Thanks for sharing. It's seems like you are using a lot of features the others may not be. It's exciting to hear about your workflow.
Are you using proxy 2.0.2?
Have you tried the newest kernel
There aren't any tasks that CloneDeploy creates that run every month, or ever. Perhaps the database program itself is running some type of maintenance.