Antique quilts had loose cotton placed in a layer and quilted closely to keep it in place. I don’t know of anything you can do to unclump it since it is not connected like modern batt.
The only reason I am hesitating on taking it apart is because it was made by her grandmother and I hat for her to loose all the hand stitched quilting on the quilt
It does sound like it will need to be taken apart to fix it right. You will at least be able to save the top and make any repairs on that before putting it back together.