When you make changes in the downloaded version the changes are only saved when you choose to save them. The save will overwrite the file of the same name so if you want to save the return in various states of completion you will need to change the file name somewhat to differentiate the files from each other and preserve each file. So if you use the "save as" option you can make as many different files/versions that you want to but be very careful to file the correct return ... that you file the finished return and not an earlier one.
One way to do this is 2016 version 1, 2016 version 2, 2016 version 3... or 2016 income only, 2016 income + deductions, 2016 as filed, etc....
