Im not an expert, but I've installed win10 twice, both times with a fresh install. Though both times I've had more than one HDD/SSD in the system, I'm thinking perhaps MS checks the other HDD's to see if the licenses are valid.
One thing to watch out for though (I wrote about this a few months ago here) In the process of installing it from USB (DVD also no doubt) it will reboot (so dont walk away whilst its installing), you must quickly enter the Bios and disable the USB (or pull it out) or else win 10 will get reinstalled again, i.e. it ignores that you've already installed it. They might of fixed this though by now, as its a nutty error on MS's part to make.