You should not have your shipping costs figured that way. It should be calculated for one package. Then, you might put some instructions on the order page about how shipping can be reduced if the customer will accept the yardage cut in pieces. But, most people who order large amounts of yardage usually have long projects that are ruined if they have to be pieced.
If you have it posted prominently about shipping in 6 yard pieces though, then she should not have reason to complain. Do you have it posted?