You lost me Jeff. Best you get some rest & post it again lol.
By changing B3601 you do in effect change all the commanded fuel tables when the tunetool is reopened. Are you saying it will not change in the PCM due to the preferences being locked?
While it may not be a dramatic inaccuracy, it will explain how returning to closed loop may lead to positive or negative fuel trims, or inaccuracies when the commanded AFR is changed.