Well, this goes beyond my expertise (not that I have any!
), but I think you have to have something in place already in order to do anything like that (such as one of the ftp clients).
Since the drive isn't physically write-protected, you may be able to fix it by deleting its partitions (When you format an emunand, it creates 2 partitions, one for the emunand and one in normal FAT32). A normal computer can't read the emunand partition, you can only see the FAT32 one.
Let's get some general information just to make sure everyone's looking at the same thing!
What console model are you using? (3DS, 2DS, n3DS, etc)
What type of SD card? (since it has a switch, I'm assuming it's a full-size)
What capacity is the SD card? (Emunand cuts off 1-2 gigs of space from the card total)
Does the SD card function properly in the 3DS?
Does the Emunand load properly?