Your other files on the sd card should stay there, 3dsx,cias folder etc. So no worries about them.3) Will this wipe any memory on either the SD or the Nand? I want to make sure my game saves and homebrew stay safe.
You only need to backup the "Nintendo 3DS" folder, and the movable.sed & some others (can't recall which specifically) in GodMode9, might tag @godreborn for that . They're essential if you want to decrypt your saves from the "Nintendo 3DS" folder..
Make sure to test it with h2testw before attempting anything, a faulty or defective sd card will only complicate things..(and i'm a little against waiting 2 hours for my shitty, slow microsd to finish backing up on my PC right now. If i do that, it'll be because i'm switching from my 16 gig to my 32 gig cart.)