The files in the root_fs2.vp do not change. The new files that you have edited will override them. That is assuming you have saved them to a directory within your freespace 2 install directory and selected that directory using the launchers MOD feature.
Also make sure windows (assuming you use it) shows you the real file extensions. You can check it quite easily. Go to My Computer and select 'Tools' from the top bar and from there 'Folder settings..' (or something similar.. i don't have English version of windows myself). Select 'Show' or 'View' from the new popup windows top bar and search for option named 'hide known file extensions' make sure the box in front of that line is
unchecked. Either do this globally or to at least in the directories where you save the table etc. files (all freespace related directories).
In general saving modifications to the main data directory is a very, very bad thing as these may interfere with any mod you might later on try. So always place the edited files into their own, separate, mod directory. So if you have installed the freespace to
C:\FreeSpace2 you would save the edited files into
C:\FreeSpace2\mymod\data\tables and then select the 'mymod' using the launcher. If you would like to use mediavps with your newly created mod you should then also use the multimod feature. That is create a text file named
mod.ini into the
C:\FreeSpace2\mymod\ directory and make it point to the mediavps directory.
Example of mod.ini assuming you have placed the mediavps into
C:\FreeSpace2\mediavps directory.
[multimod]
secondarylist = mediavps;
For more information...
http://homepage.ntlworld.com/karajorma/FAQ/installingmods.html