Hi alondon,
I am not with Laminar Research; just a flight simmer.
The process of deleting one version is quite simple and you don't need any fancy software to complete the task.
Provided you have either loaded a version onto the desktop as per the instructions in the manual or onto a dedicated drive or as a dedicated directory ie no other file/program files, then all you have to do is use the delete command and it will be removed totally. The proviso is that you have not mixed X-Plane within other file directories.including your operating system files.
The version you select is your choice. As i read your problem your first version is the one you want to keep.
When completed you only require one LIcence for the software.
As a sideline issue you never have to reinstall the software from scratch ie delete and then install. All you need to do is run the installer file and it will find the location of the software and check for missing or corrupted files and either add or replace the necessary files.
Good luck .
Glenn