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At this point I just accept that my windows desktop is going to reboot itself and update itself every fucking night. I used to be able to leave it on for months at a time only rebooting when I felt like it and had prepared all of my open projects to be rebooted.
Now I do those projects on my Linux PC, which has to be a separate PC now because the windows updates completely screw up dual booting. Microsoft is such a shit show, I would probably only turn on that PC on the weekends except I need Windows for work.
Put a second hard drive In your PC and install Linux solely to it. Then you can use your BIOS boot menu to choose which OS to boot and Windows can't wreck GRUB when updating.
I thought that too. My (now windows only) computer has two M2 slots, I used one for Linux and one for Windows. One day I walked into my office having left windows running the night before and my computer had rebooted and updated, The first thing I did was try to boot into the Linux partition and it did not work.
Not taking that chance again, I now have two separate PCs on my desk.
Hmm. That's interesting. The only thing I can think of that could potentially cause that is if for whatever reason there was an exisitng EFI partition on your linux drive. Windows will use whatever EFI it sees even if it's on a separate drive from it's primary NTFS partition. As you can imagine this can cause some fucky stuff to happen.
Some instructions I've read for dual booting recommend installing Linux first, removing the SSD wit Linux on it from the computer, and then install Windows to prevent that from happening.
It's really shitty that users have to go through all that trouble, though.