I would put a note on the checkout page to your customers: If this situation arises, would you rather a) we save you money or b) send the cheapest way? Even better if there is a box on the checkout where customers can place comments: "Please do not cut "blue roses" no matter what, but the pink fabric could be cut if need be;" or "Please send all one length, even if the postage is more."
I have ordered fabric online, and have been contacted that they were out of all one length, and would 2 smaller cuts be alright?
Also, since I live out in the toolies, we lose internet connections all the time, sometimes for days on end. Doesn't matter how often we complain about it, so I know what it is like to miss important emails.
If I have a question, I contact the seller ASAP, if I am able to do so. If not, I figure they did what they could, and live with it. I also deal with sellers that give me free shipping and will take items back if I am not satisfied. Of course, it's not international, so I know that makes a huge difference.
All in all, I expect I would have held the merchandise, or sent all one piece, provided she had agreed to the higher shipping rate.
It was a tough call. I'm sure you did what you thought best for the customer.