FATE doesn't truely know that Lucca created it. Neither does it know that Belthasar is using it. FATE was given the task of watching over El Nido, without knowing of what would happen (Schala's interferance, Serge's Arbiter status, The Prometheus Lock etc.). If FATE did truely know the whole course of time, then it'd know that Belthasar was using it, it'd be destroyed one day etc.
From what I remember, Lucca worked on the new circuit board so that if Belthasar took it to 2300AD (if they ever met) or if it was found in the future, it'd make sure that most of the Mother Brain rougness would cease. As for the Prometheus Lock, (And Kato did say that it is Robo), it could have been that Robo stayed with Lucca, or she brought him back, and he voulinteered to become the circuit or something.