Richard, congratulations on a successful mission.
As for the pref files, generally what happens in the flow of things is the first time you launch some application program, a preference file or files are created by the application and placed usually within your Library folder ~Library/Preferences. Those are prefs specific to you. Local prefs, rather than global prefs.
If you then subsequently go on to change some preference within an application, such as changing the point size of the default application font for example, that change is stored within the pref file. On occasion a pref file can become corrupted, even to the point of the application being unable to fully launch, or making it freeze. In my example lets say you removed the default font you set your preference to.
We as technicians generally know where to go to find those prefs and we will set them aside and allow them to recreate as a way of troubleshooting and hopefully solving problems. You are "generally" ok doing that with application preferences, but you really need to know what you are doing when you start managing more system related preference files. I mention all of this because those prefs that you removed should become recreated if you were to launch those parent applications again.
It's always good to have patients and ask questions before making changes that may affect the way your computer functions. You score high marks on that and are now rated as a super user, :-)
Take care,
Tim