At the moment, there isn't a way to change the quantity on an invoice that is linked to an estimate. What we can do, is to delete and recreate the transactions and manually reenter the correct quantity.
In the sample co, you CAN change the quantity on an invoice that is linked to an estimate. When you click Save you get the message: "The transaction you are editing is linked to others. Are you sure you want to modify it?". When you click Yes, it saves