If you want to mantain your sysnand installed content, backup the Nintendo 3DS folder, than format the SD with SD formatter.
Then copy back the Nintendo 3SD folder on the SD. If your sysnand and Emunand where unlinked, you'll have to delete one of the two folder inside the Nintendo 3DS one. You have to find yourself which one is the good one, but if you delete the wrong one you still have the backup
If you want only an empty SD, simply format it with SD Formatter.
I've done all this and I still have that extra gig or so that it wont format. I have a 32GB SD card and normally formatted it's left with about 30gb but now it's at a little above 28GB
I use easeus partition manager. The free version can delete all partitions, and reformat it to one single partition drive. http://www.easeus.com/partition-manager/
Also thanks guys, I wasn't sure if partition managers could read the gateway partition or not.
the technical term for the unallocated space on the SD which is a partition (which when you make an emunand allocates data) its just read differently its not really unallocatedCorrectly speaking the emunand isn't in a partition, but in an unallocated space of the SD.
For a Partitioning tool it's only empty space. Wipe out the main partition and for the PC the SD will be empty and unpartitioned.
download SD FormatterI've done all this and I still have that extra gig or so that it wont format. I have a 32GB SD card and normally formatted it's left with about 30gb but now it's at a little above 28GB
the technical term for the unallocated space on the SD which is a partition (which when you make an emunand allocates data) its just read differently its not really unallocated