After you file

If your 1040 is incorrect, do they send it back to you to be corrected and refiled??
Of course not.

Same goes for 1040-X.

They know they already refunded the UCE portion, and your 1040-X overpayment(refund) will be adjusted.

 

P.S.

My niece is waiting for a 1040-X and an adjusted reduced refund for exactly this scenario.

They're not going to return her 1040-X to her. Besides, she e-Filed it.