Merging doesnt always work to well, a better way is to rename the file (if it was 440003) make yours 440004 or what ever and then find the main script (that uses the 440003.xml) that you renamed to 440004.xml. and add the "Load TEXT:ID=4" to its script. (init.mk2.bindCommands.xml)
an example is the "Trade Command Software MK3" and "Teladi Auto Trader Mk2.2c" both use the 440003.xls.
to fix it so that "Teladi Auto Trader Mk2.2c" uses your new file 440004.xml you need to:
1. Rename the old 440003.xml to 440004.xml (right click and rename)
2. and this assumes that you have already enabled the ingame script editor, if not go into open space and type "Thereshallbewings" all 1 word, Capital T, no quotes.
once enabled access the script editor (if in space) press S then C, then S and follow the prompts. once in the editor scroll (using the "down" arrow on the keyboard) through the scripts until you find "init.mk2.bindCommands" and press enter while it is hilighted.
3. you are now "editing" the "init" (runs automatically everytime the game starts) script for the menu selection/options (ingame) for the script Teladi Auto Trader Mk2.2c.
4. scroll down to the 001 line and press "insert" on the keyboard, this will add a new line where you can add a "call" for the newly named .xml file.
5. press enter on the new 001 line and select "general commands" scroll thru these commands untill you are 7 from the last and select it (load text:id=<var/Number>), once you found it press enter and you will be given a "Script Input" screen, scroll down to "number" and hit enter, then type in 4 (if you renamed that old file to 440004.xml) and hit enter.
Hit "ESC" and choose save and the script will work next time you start the game.
The info is now added to the script and when you restart your game the menu options for Teladi Auto Trader Mk2.2c will now be available in the in-game menus.