I hope I'm understanding the problem. Can you pull the piece on the diagonal to bring it back into being square? Sometimes that helps. It depends, too, how badly this is out of square but I usually don't worry much about this with quilting. In my days of garment construction, we did have concern for pulling a thread to make yardage square but I don't find that so much with quilting. I don't know what makes the difference. Perhaps because we are stitching/securing the fabric closely to the other layers? But it doesn't seem to make the difference that it did with how garments hung.
Perhaps you can steam press this back into shape. The way fabric goes onto the bolt can pull it out of square.
But, if it isn't bad, I square according to the fold so it is smooth, bring the selvages together and square using the rotary cutter and move on.