I assume you have updated the software, right?

Does it prevent you from entering the number or does it not calculate the amount?  If it otherwise works, just ignore the warning.  You might not be able to e-file (whenever the ability to e-file amended returns becomes available), but if that is the case, just paper-file.

Is there a reason why you are amending rather than filing a 1045 (or 1139) with the current year return (or faxing it with the special provision for this year)?