Assuming you're talking about the G6 Lite, you can just wipe the cart. The only folders you need are /NDS/ for DS games, and /GBA/ for GBA games, and the U-Disk Manager will create both folders for you.
You can delete the .1 and .2 files the U-Disk Manager creates if you don't use the multiple save feature (don't delete the .0 files, those are your main saves).
The .is0, .is1 and .is2 files in the /GBA/ folder are for the real time saves (save states). Delete them too if you don't use them.