What you are referring to, is the discovery process.
When a scenery is installed using the add-on.xml method AND the add-on.xml is located under Documents\Prepar3D V4 Addons, which is the case for all our products, if you Uninstall the sim and reinstall it, even from scratch, and even by clearing up all its files, including the scenery.cfg, if you don't remove the Documents\Prepar3D V4 Addons folder, when the sim will first restart after a complete reinstall, it will search for all add-on.xml files and will ask if you want to activate each product.
This will save you from having to run all these products installers again.
If, instead, if you upgrade the sim JUST by Uninstalling/Reinstalling the client, this wouldn't even be an issue, since the preference are not usually removed when upgrading. But of course, if you want to upgrade and clean up and remove the preference files anyway, as long as you don't remove the Documents\Prepar3D V4 Addons with all the add-on.xml that are located there, the discovery process will start too.