OK, Microsoft....you say that you are making peace with and coexisting with Linux.
However, you still don't play nice with it. :-(
For years, we all knew that you had to install Windows first because you didn't play nice with others, then install Linux afterward, with its GRUB bootloader that lets you boot just about any OS.
Well, I made the mistake of allowing the Windows 10 Fall Creators update to happen on my laptop while I was away on a business trip...without my SystemRescue USB drive or Linux live CD. You guys killed my GRUB bootloader, and I can't fix it until I get home. This cost me a day's worth of work fixing a couple of remote co-located servers, since all of the tools I need for this run under Linux.
I took a look at the EFI partition with bcdedit /enum firmware, and it seems that you apparently overwrote GRUB in my \EFI\ubuntu partition - since I tried using bcdedit set to change between the filenames in the \EFI\ubuntu partition (which is first in the boot order) - still goes straight to Windows. Tried doing the same with a third-party utility called EasyUEFI. No joy.
Can't you set up the Windows Boot Manager in another directory in the EFI partition and (if you must), just point to it instead??
Or, if you have to modify the bootloader to allow for the several reboots during the upgrade, just store the original setup, then restore it when the upgrade finishes?
Better yet, just let me use GRUB to boot into Windows after each step of the upgrade.
For next time, please consider this instead, and learn to play nice with others! We know you can, if you decide that you want to...!