@readerBig: The "whole setup" doesn't actually disappear, unless something is going seriously screwy, as @davidfor explained

. Out of what ships w/ OCP, only KFMon gets disabled (as the first NOTE explains).
(i.e., you'll at least have to reinstall KFMon after an update. The rest of the OCP tools (NM & KOReader/Plato) do survive).