Capcom’s Resident Evil: The Mercenaries 3D along with a few other Nintendo 3DS games like BlazBlue: Continuum Shift II have permasaves. While you can’t reset data directly, there is a way to wipe a cartridge.
The NDS Adaptor Plus was designed to back up save data from Nintendo DS and 3DS cards to a PC. You can also use the device to erase any game saves. It’s a little bit of a hassle, but if you want a fresh copy of Resident Evil: The Mercenaries 3D or any other 3DS game with a permasave, there is a solution.
Thanks to Stefan for the tip!