So I literally just dealt with this. However I purchased my device from AT&T, not Apple. However perhaps my story will help with yours.
AT&T received my return yesterday and sent me an email this morning that they had received it. I then had to call AT&T and tell them to please process the return so that I could be freed of my contract on the returned device in order to be able to pre-order a new iPhone this Friday.
After about 10 mins, with the help of supervisor communicating with my CSR, they were able to do this.
Your situation is different in that you returned the device to Apple, not AT&T. However as long as you have proof that Apple received your return, I don't see why AT&T cannot remove the payment plan at this time.