I am having a similar issues - I made a mistake on my original filing by having a wrong box check on an IRA. I notice the issue after I filed. I found the problem by unchecking the box. I then went to do an amended return and the dollar amount of my return was set to the right number but the box was checked that I had unchecked.
When I unchecked it again it took my return to zero. I don't see any options other than doing a new tax file. But I am sure that will cause an issue if I file twice.
