And this is why you NEVER amend (not superseded ... that is a business return designation only) a return before the original return was fully processed ... that was the reason for NOT letting you amend too soon. If this is for a personal return then you should have mailed in a form 1040X (not an original 1040 with red letters on top) so although the check you sent was cashed right away it is highly unlikely the new 1040 will ever be looked at ... if it is it will be months from now.
Now if you did mail in a 1040X was the amount on line 18 the original refund you did get ? If so the IRS will eventually process the amended return and all will be right.
If you sent in a 1040 by accident then WAIT for the IRS to ask what that payment was for ... only then should you respond with the correct 1040X form ... please don't jump the gun again and make things much worse.
