A problem like this would almost certainly be detected. If it is not easily detected then it is almost certainly not a problem.
If the skipping occurs randomly then it is very unlikely you would get the same number of skips on 4 calibration rides. If there is a different number of skips on any of the rides it would give a large count difference (at least 10 counts) for one of the rides.
If the skipping occurs in a regular pattern, say one time every 20 revolutions, you'll get the same count number for every 300-meter calibration ride, and the skip will go undetected. However, you'll get the same count number for every 300 meters of the course as well, so the course measurement will still be accurate!