The game is going to automatically re-patch every time you log in and since the files you "created" are different from the ones that are "supposed" to be there, the system will self correct to bring you up to date. It may be looking at file size or possibly file creation date or even both of these but the bottom line is that if the files don't match, out they go!
With UI mods, you are putting all the replacement files in a different directory - one that isn't patched by the game system.
Long term, your best bet is just to turn down the in-game music and run in windowed mode with an mp3 player up for music. I often do this when I'm crafting. I also like to run Pandora radio when I'm doing something mindless like grinding writ mobs.