The portable version you download is packaged in a way that you can always just unzip it on top of your existing portable version to upgrade.
The only time you have to be a little careful is if you are going from a portable to install version, or vice versa, and want to preserve your settings.
In this case, the trick is simply to make sure FARR looks in the right place for your settings and customizations. The ConfigDir*.ini files are what tell FARR where to look for its settings and where to save data.