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After you file
I called Turbo Tax and they indicated this is the correct behavior. I have to "recreate" the data exactly correct so that it only adjusts the changed entries I need to make. Problem is I incorrectly answered a "Yes/No" question way down in a Schedule E worksheet. So far I can't seem to figure out how to even get to the point that it "recreates" the worksheet and gets to the same question which would then lead to a whole set of other changes. I don't know how it knows how to propagate these changes to other affected files. It seems I have to determine what other files need to change to actually then modify these other files, which are only created based on the other data values I entered.
It might be possible to do an amendment this way, but it seems to be way beyond my capabilities.
I thought I'd try some simple change like change my address in an existing W2 and the first question it asks, which must be entered is the Box 1 content of the W2. I did so and made no other changes other than the address. In the 1040-X, it said I had a new income based on the Box 1 entry I made and then calculated a new tax liability just for the W2 data I entered. I have no idea how it can calculate a new tax liability without knowing the previous return data (i.e. what tax bracket I would be in, etc). Why did it even think it was a missing W2? I just don't understand how amending works.