So if I use this program in theory I can take the SD card from one 3DS and mount it's contents in ninfs, then literally just copy a save from a lost 2DS to another 3DS SD card and it would work?
You just need to format a 4GB+ using this tool, https://www.sdcard.org/downloads/formatter_4/ , format your SD to FAT32 and use the Full Format option. Success varies with every SD card but all sizes should work, I've had several 4GB and 8 GB cards work.