You have to remember that the engine was built for the Yamaha R6, so it's likely that there would be a mounting point that isn't used on the FZ6 and I remember somebody else mentioning on the forum a while back that the hole was a mounting point for the R6.
Thanks for posting. I noticed it the first time I rode and wondered "what fell off"....A hole that big had to be something important. Mount for another application makes sense.