There was noting wrong with sending in a superceded return EXCEPT that the IRS would process the original return way before they could process the second return. So them sending out the original refund is to be expected as is them cashing the check for the balance due on the paper filed return. Eventually they will get around to processing this "superseded" return and pairing it up with the payment you sent and send you out a notice asking for the all or part of the original refund to be sent back ... please wait for the IRS to catch up in this matter and expect it to take 6 months to a year to process everything.
Next time wait for the original return to fully process before sending in an amended return or a superseded one as you can see not waiting is causing confusion.
