Going by the Marvel wiki, the Otto Octavius that's appeared since The Clone Conspiracy is referred to as "Otto Octavius (Duplicate)," since he is technically the product of a digitized copy of Otto's mind being uploaded into a cloned body of himself (and then of himself and Peter Parker mixed together) and thus not necessarily the "original" Otto restored. That's probably why the appearance list for "Otto Octavius (Earth-616)" hasn't been updated with the Clone Conspiracy-onward appearances.