Not sure if others have already posted this, but in case it saves someone some time: I found that I didn't even need to restore the actual Windows Boot Loader (I'm dual booting but with both OSes on the same disk). Instead I only needed to set the boot flag on the Windows partition (rather than it being on the Linux one).
This still left GRUB as the loader (as it's installed in the MBR), but seemed to do the trick for the update. For reference I triggered the update from windows, then let it reboot and again selected Windows from the GRUB screen.