A System Format will unlink your NNID and uninstall all software except the default system titles (the stuff that comes on a brand-new clean 3DS system), but you can just re-link the NNID when you're done and re-download all of your legitimately-installed paid eShop titles. You can also backup digital game saves through System Settings/Data Management, although I don't know how useful that will be in this case, or whether it backs up to Ninty's servers or just a separate save file on your SD. I also wouldn't try it with games you don't own. The process of using JKSM might be a bit slower on homebrew only, but you're pretty much guaranteed the ability to restore your saves no matter what, although there are some troublesome games on 11.1 (Pokemon ORAS are the only ones I've heard of that outright fail, due to a new save data thing). From personal experience, though, I can tell you that restoring saves to Devil Survivor 2 through JKSM will fill any empty save slots with junk data that will crash the game if loaded. Pre-existing saves work fine, but it took me a while to figure out that it hadn't corrupted my save files... XD