I had to amend a 2013 return a second time. This is what I found.
To do a second amended return you need to use the Desktop CD/Download program installed on your computer. You start with the first amended return and try to delete the 1040X and state amended forms. I couldn't make that work so I had to start over with a NEW return. You need to make a new return that would look like what the return should have looked like after the first amended. So that will become your new "original" return. You can save the real original return with a new name and update it with the changes from the first amended return so you now have a new "original" return to start with. Be sure to save several times along the way and make copies to work in, in case you need to start over and try again. THEN when you have the new "original" return you can Amend it. You will probably need to enter all the prior refunds and/or tax due payments directly on the 1040X (and on state) using the Forms mode. I had to enter both a tax due I paid on the first original return AND a refund from the 1st amended return.
Basically, to do the second amended return you have to start with a dummy "original" return that incorporates the changes that were made by the first amended return. Then you can simply go through the normal amending process. There are two ways to produce the dummy original return. Both ways are hard to explain and to understand.
One way always works, for both federal and state, but it's for desktop only, and you have to have a copy of the .tax file for the actual original return that you filed, before the first amended return. You make a copy of the .tax file for the original return with a different name. Open the copy and make the changes that you made in the first amended return, but without going through the amending process. That gives you an original return that incorporates the changes from the first amended return. A variation of this method, if you don't have the .tax file for the original return, is to create a new return from scratch, reproducing the original return. But that's a lot of work and very error-prone.
The other way is to open the first amended return and delete the Form 1040X. That will leave you with what appears to be an original return, but incorporates the changes from the first amended return. This will usually work for the federal return only. In theory it should work for the state also, but some states don't let you delete the amended form, or it immediately comes back after you delete it. Sometimes deleting the state amended form makes the federal 1040X reappear. The results vary for different states, and sometime vary even for the same state, depending on the exact sequence of steps that you follow. With some states there seems to be a problem even deleting the federal 1040X.
