Hi, chairgaf. You never "lose" points. However, when you miss a calibration, your skill level takes a hit as indicated by the blue bar dropping a bit. The number of points you receive for "correct" responses, as you know, is directly proportional to your skill level. So, when your blue bar is at maximum, you get 116 points for non-calibration movies, 2320 points for flow calibration movies, and either 2320, 4640, 6960, or 9280 points for the various stall calibrations. If your skill bar is at half mast, you would expect to get half those numbers of points.
So, when you 'miss' a calibration, and your skill level drops a bit (which varies, better to miss a flow than a stall), you could say, "Well, I was getting 110 points per regular movie, now I'm only getting 98; I'm losing 12 points per movie." In that sense you are 'losing' points, but points are never deducted from your score.
Hope that helps.
PS. For advanced players, there is a bit of an exception. If your skill bar has been at max for some time, when you finally miss a calibration, the bar might drop much less than you'd expect, or perhaps not at all - no penalty. Miss again soon thereafter, however, and watch it plummet!