After noticing that it is indeed possible to write and use more than one EmuNAND from a single SD card, thanks to the efforts of nop90 at reverse-engineering the Palantine CFW, I decided to write this little tool for Windows in hopes of simplifying the process as much as possible, since I think no one has done it yet....
[RELEASE] 3DS Multi EmuNAND Creator
[RELEASE] 3DS Multi EmuNAND Creator