It's possible that your cart is not legitimate, bootleg/reproduction carts often have this issue of not being recognized properly, because their internal structure is not identical to an official copy.
You may have to find a NDS cart reader/writer to properly extract what you need, and even then it may be difficult to obtain your save in a readable format, and potentially even harder to edit and then replace.
There are many guides online you can find to identify counterfeit NDS carts, especially Pokémon games. I suggest double checking your cart's legitimacy, as reproduction carts have even been accidentally resold "as legitimate" by certain retailers who couldn't tell the difference.