I have moved this to the main NL board as it is not a bug or suggestion. In terms of your actual question, Icho summed it up pretty well.
I do recommend installing to a clean folder if upgrading from one major version to another (eg. 12.11.X to 12.12.X). You can still copy levels and progress from your old install. When upgrading between minor versions (eg. 12.12.4 to 12.12.5), you can install over the existing copy, and I generally provide upgrade ZIPs that contain only the files that have changed.
If you are upgrading from a really old version (10.X.X or 1.X), you should set up a completely fresh install as most files are not compatible between those and 12.X.X.