Someone may have picked it up.

Did you take the note by the skeleton before, and was it there again when you went back? If so, the map refreshed and probably erased the mask.

I had exactly the same problem as you and have fortunately come up with a solution that worked for me. After spending about an hour fruitlessly trawling around Labrynthian I decided to leave the Nahkriin mask I had in my inventory in the exact same place I had originally left the wooden mask before it disappeared. I then fast travelled to somewhere and then fast travelled back to Labrynthian again. Lo and behold, the Nahkriin mask had moved a few metres across the floor and the wooden mask was back in its proper place. Perhaps one of the happiest days of my life. Hope it works for you!

For the PC version go to the console by pressing the tilde ~ and type player.additem 00061cca 1 the mask will be in your inventory.