No they are not taking your return at all. An amending your taxes resets the amount owed/refunded to 0 but keeps all the information you already filed with. The reason it resets to 0 is because the software is made to believe you have already sent your taxes to the IRS and either received or payed the amount owed with the information given.
You will receive your refund but you will need to pay the $12 you owe.
