I just saw, that Fn + something generates VK_Something. It seems to solve the case.
Of course does pressing Fn + function key generate VK_functionkey. That's how it works.
But you didn't
detect if it was pressed with an Fn key. You just detect if the function key (F1..F12) is pressed.
If that was all you where after, you didn't need to ask about the Fn key because that doesn't matter.
On some keyboards you need to press Fn in combination with F1..F12 to reach those function keys. Otherwise you get other functions. For the ultimate scancodes which you receive from the keyboard, it doesn't contain information if it was in combo with Fn.
BTW. If you don't like the Fn key, some systems let you disable it in the BIOS so that pressing the F1..F12 will directly activate the key as function key.(without the Fn).