A few people have reported troubles taking files off the ds-x once they're done with them. Dragging them to the trash wouldn't work and would still be taking up the space. A few ideas were mentioned, but one idea posted seems to be the easiest.
If you Hold down Command (thats the Apple key) while dragging your .nds files to the Trash, you will Move it to the Trash bin and it will be gone from your DS-X.
You can find more on the topic here: ds-x thread