1) Close X3Editor and Plugin Manager.
2) Back up your entire X3 folder. Just in case you ever need to revert to previous files.
3) Open the Plugin Manager (to remove its merged files).
4) Open X3Editor. Make sure that your X3Editor profile is set up correctly, including which game you play.
5) Open from VFS to get the correct file that the game will use.
6) Double-check the path to the file in the X3Editor title bar.
7) Obviously, save when done editing.
8 ) Close the Plugin Manager (to allow it to rebuild its merged files.)
There are some videos demonstrating the above (and more) in the Ship Tricks tutorials in my sig. The tutorial about File Precedence will explain why there are multiple versions of files and which one is used by the game.
- (The steps with the Plugin Manager (PM) are only necessary if you merge anything. Examples are .xsp ships, or EMP if you are editing TWareT. If you are only editing TShips (and have no .xsp ships installed), then you can safely skip the PM steps. )