The (vanilla) NPCs are only deleted if you use JPAN's patch. You can use the application that's included with the download to choose what you want or don't want to include so it should be fine if you use that instead.
Well, I tried the tool but I understand that I have to set a variable for every single trainer battle individually? I can't make all trainers have levels the same of mines with just clicking a button? I have to edit EVERY trainer of the game and add the setvar to EVERY script?
I remember a patch that sets all trainer's Pokémon's levels automatically.
Nope, once you set the variable, that's it. If you set 0x4052 to 0x100, every trainer battle will have the same level as your highest Pokemon until you change it to a different value. The variable isn't reset after battle so there's no need to worry about it~
Well, I tried using the tool. Ticked the right box, that opens a box. When I set 0x100 it does notging and the box moves. When I write 0x4051 it switches to trainer battles, then I write 0x4052 and it closes. I never got the chance to write 0x100.
Maybe I'm getting something wrong (English is not my mother tongue btw).