If you used the 2016 desktop version to prepare your return, then you can use the same software to amend a 2016 return as well.

You would just use the same program.   Or did you uninstall it?  If you uninstalled it, you would have to reinstall it in order to amend a 2016 return. 

There's no reason to uninstall the software unless you are really crammed for space.  I have 3 years of TurboTax programs installed and can easily open a past return or prepare an amended return if I need to without having to install anything.