I agree with everyone's posts...
Definitely take a "before" picture.
Definitely show the LA'er. As a LA'er myself, I would be HORRIFIED to know that the batting did this!! I would immediately figure out some way to make you (my customer) happy. I would want to know so that I don't use this batting ever again!!! And as Jane Quilter said, offer to "skin" the quilt yourself, and see how your LA'er reacts as far as reparations go.
Good luck with the skinning/frogging. Yes, it's very, very sad, but you will be glad you did it in the long run.