If you measure a course with two continuous rides from start to finish or vice versa, there is only one way to make a comparison.
If you measure a course in a segmented fashion there is a multitude of ways you could compare the multiple rides, and the decision was made that it should be done in the most conservative way possible. That is, taking the minimum count for each segment.
If one ride is continuous and one ride is segmented, then you are back to only one way to do a comparison, and that's what you should do. No certifier should make you do a third ride just because you went the wrong way briefly, and because of that created a segmented ride.
Note that whatever method you use to fix a wrong-way mistake, you are technically creating a segmented ride.