After you file

Did you actually file the amended return BEFORE you received the original refund ?   If you did bad move... you should have waited for them to process the original return and sent the refund before filing the amended return.

 

And then you filed the amended return and directed the balance due to be debited  AND  they did as you requested.  So review the amended return ... are you sure it reflects the original refund on it (line 78)  or  does is simply show the current balance due ?