There's a program called 'intro remover' that was designed to remove the tacked on intros by the people who released the roms (GBA ones), but it can be used for removing trainers. I've never tried it on a DS rom, but I have on GBA roms.
I don't know where I got the program from so my suggestion is to search google, but there's no telling if it'll work properly so I'd back up my rom before doing that.
The other suggestion is to re-download the rom. It'll save you some time and grief.