If you look at your sd card with a partition management tool (I use EaseUS), it should look something like this:
[=====|+++++++++++++]
Where = is labeled unallocated space (this is actually your Emunand but it doesn't know how to to read it so it calls it unallocated) and + is your normal filesystem that holds your regular 3DS files. What you can do is right click and do "resize partition". Drag the bar from the left edge of your main filesystem all the way to the left side so it takes up your whole SD card. Should look like this afterwards:
[+++++++++++++++++++]
With the unallocated space completely gone. This SHOULD remove your Emunand but keep all your other files and give you your SD card space back. I did this about a week ago when i wanted to delete mine just to test it (I did back up my SD though first just to be sure.) Do NOT hold me responsible if this messes something up! I am just telling you what worked for me. USE AT YOUR OWN RISK!