"The only logical explanation for this conflict is that Alaska has reversed its opposition to the state investigations (which is good), but does not wish to affirm such by rescinding its endorsement of the June letter (which is not good)."

Or there's the possibility that Ms. Lindemuth is telling the truth, and that the she wants to ensure that the principle of litigating these investigations in state courts is upheld while still agreeing that these particular investigations are inappropriate.