I've just done what I put aside for a long time. Backed up my saves first, then all I did was delete the sx folder and a few files, copied over atmosphere and updated the apps that needed updating like fpt, save manager... copied over the all in one updater. Then I updated the firmware from 11 to the latest....it all seems to just work without a hitch. Now I need to figure out the best and easiest way to install games, updates and dlc. And get the freeshop thing working.