[Kusuri]

Best Thing you can do is to jailbreak your kindle and then install a FileBrowser so you can delete the folders manually. KoReader is also nice since you can wipe the .sdr folders etc.

And for the future.. i recommend using a neat folder structure to sort all books you have, that makes it a lot easier to manage this kind of stuff. i as an example have an folder for mobi files and epub. And in this folders i have folders like "Fantasy & Light Novel", "Science" etc.. and in this folders i have individual books in their own folder. So if i am done with reading a book, all i have to do is move into the folder, delete it, done. since it sorted its relative easy to find and delete this folders when i sideload new books onto my kindle. so i usually only delete this empty folders when i am loading new books onto my kindle.