You can solve that problem by making an additional efi/boot partition when you install Linux over the Windows install.
You have Linux setup with its own boot partition and the install should probe for a foreign OS, it then adds a chainloader entry in grub to point to the Windows EFI partition.
You set BIOS to boot from Linux EFI partition. When it comes up at boot you can chose Windows and Grub hands over control to the windows bootloader, but Windows is ignorant of Linux EFI existing. It now only messes with its own EFI and never touches the Linux stuff.
@utnapishtim