“The factory said they still have some old cartons in their inventory. Can we use the old version cartons for your order? It will be no problem if we can’t.” That's fine. There are many ways to word it, but your way is fine. The meaning of "old" is not clear in the first sentence. Filled in a little in the second. It could mean labeled for a previous model. It could mean falling apart. You might want to reassure. “The factory said they still have some old version cartons in their inventory. Would it be ok if use the old version cartons for your order? If this presents a problem we can use only new ones. Please let me know.” ... many ways to go. :)