Finally after many tries this has now been resolved. I got another agent who was more helpful. By removing the AS-flight my OK number could once again be entered without it being incorrectly denied by DL. After this the AS flight was again entered into the itinerary. However, my status was still not reflected in the Delta-system until the agent cleaned out the old error messages saying the number was not accepted. So my reservation has been fixed now (unless I dare change the FF again).

However, the problem still exists. DL computers deny some Skyteam-frequent flyer numbers in the whole reservation when there is a DL-coded AS-operated flight in it. This is incorrect as I will earn miles to OK as normal, they do not care about operating carrier (which is the best way all programs should do it).