That is not acceptable at all. If your customer wants cotton batting, you use it. I have a LA there really is not alot that you have to change to change the loft of the batting or thread for your tension. it's maybe a 5min process. Did she atleast return your batting to you and your thread? I'd be finding a new person for sure. It almost sounds like she is rushing your quilt to go onto the next. Most quilters go by word of mouth when picking a LA quilter and this would not make her get any additional business.
I did 2 for a friend at christmas and she sent the thread that she wanted me to use so I used it but there wasn't enough so I did as close as I could to the spool that she provided. I wouldn't think of using something that wasn't close to what she wanted or calling to confirm the change before I started.