The cal course in front of my house is a little short of 400m and rises about 5m, most of that in about 150m at one end. The counts going in one direction will vary by 1 or 2 counts from the counts in the other direction.
One day I was calibrating and the counts in the two directions were consistently different by 5 counts. What the heck! I then remembered that I didn't check my tire pressure. It was only about 40psi instead of my usual 55-60. After I pumped up to 55, the difference was back to 1-2 counts.
I think there is a good bit of individual experience to suggest that riding a cal course in the uphill direction will give you a different count than riding it in the downhill direction. But if you ride in both directions and average the results, will it give you the same count as a flat course. My instincts tell me yes it will, but data is always better than instincts, even when they tell you the same thing.
The interesting thing about this is that if we do find that it causes a bias, the result would be that you should use a hilly cal course if you are going to measure a hilly race course, and a flat cal course if you are going to measure a flat race course. Kind of what Jim was saying, but not the current recommended practice.