TWLSaveTool is a 3DS homebrew that allows you to read, write, and erase save files from NDS cartridges (just like savegame-manager!)
The CIA build requires an access to CFWs. If it's the case, this is the best option; you'll be able to see the awesome banner Apache Thunder made 😉.
The 3dsx build requires you to have either PokéTransporter or Pokémon Dream Radar installed on your 3DS. In both cases you'll need to pay to be able to download them.
All games except WarioWare D.I.Y., Band Brothers DX, Art Academy DS, and Pokémon Typing Adventure should be supported.
How to build
Have libctru and devkitARM correctly installed and set up, as well as makerom and bannertool in an accessible path, then run: