There might be a newer or better way but here is my notes for amending a second time.
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.
Make sure the original refund or tax paid and the first amended amounts you paid or received shows up on the 2nd amended return. You may have to override the amounts using Forms Mode.
You can confirm this by printing your amendment and looking at the 1040X. Line 18 should be your total refund amounts and line 22 should be your additional refund. If you paid on your prior returns it will be on line 16. If there is an amount owed with the amendment, it will be on line 20.
