Correct regarding 42 days (equal 6 weeks * 7 days). All days you set your feet in Denmark counts, but I don't think that a short turn around in CPH counts. But if you are staying overnight at a hotel in CPH as part of your ALC-CPH-ALC, then it counts.
My best advice is that you dont use your credit card to buy something in CPH Airport, if you have a short turnaround (that is if you have the time to go to Lagkagehuset, or JoeJuice). Dont leave any electronic fingerprint, then you will be good to go.
The reason, why I believe that a short turnaround donīt count, is that the airport is a part of your working place, where as, as soon you leave the airport then you are not working anymore - seen from SKATs point of view.