I agree, what you are describing is not what I would call a "calibration" - at least in terms of the sensor (or, to be fair, the controller if it depends on that sensor.) Conditions tested "as found" and "as left" should be identical, with the only difference between the two any adjustment (if required or possible) if you are calibrating the sensor.
If you are "calibrating" the freezer "system" (sensor, controller, and PM), then as found would be as it was found (iced up), and as left would be defrosted (as an "adjustment"), if that is how you left it. If your +/- 1 degree tolerance is for the system, and you find a 3 degree difference, then you need to correct the system (yes, out of calibration) - which (of course) is defrosting more often so that the sensor does not accumulate enough ice to become more than +/- 1 degree off.