Isn't there something wrong here where the KLM phone agents have no idea why the proposed fare for the return flight is what it is?

I had a similar problem with UA last summer where the system insisted on a re-fare for a changed return that was clearly wrong, I had to pay the money and seek a refund (which was given after a few email volleys.)

My understanding is that the fare charged the OP for the return should be based on historical fares that were available to purchase at the time the OP made his reservation, for the itinerary he would fly as modified.