I too would have been upset if I ordered a lot of yardage, and it was cut without my consent. If you cut it at 6 yds each, and what I needed was 7 yds and 5 yds, then one piece would have been unusable.
I beleive you should make a section on your webpage, that international customers need to read and agree to by check box before they can finish the checkout process, that states, how much you can get in your flat rate envelopes, and if they order more than what fits in there, the shipping will be different than your shopping carts charges, and you won't ship until they have responded to emails about the additional charges for shipping. Once you know how much they are ordering, and how much it would weigh and cost in additional postage, email them, and give them 72 hours to respond. If they don't respond then cancel the order. If this is all spelled out on your webpage, and they have to read and agree before placing the order, then they can't argue with you if the order is cancelled because they didn't respond.
I agree that things come up and people may not have internet access, but that isn't the businesses fault, it is the customers fault. You can't hold a business responsible for someones internet access. I beleive it would be better to cancel the order, and let the customer know why, and if they really wanted the fabric, they can order it again, knowing that they are going to have to approve additional postage charges before the order will be filled and shipped.
As long as you state these things on your website for international shipping, then the customer becomes responsible for making sure they reply to any email informing them of additional charges. While this may not help with the customer that this happened to, you can take steps to make sure it won't happen with future customers.