The strata manager says that not much can be done about it now.
Not much can be done if you do nothing. How about you offer the owner the choice between agreeing to a by-law that passes responsibility for the balcony to them, or they resinstate the balcony to its previous state at their expense. When they refuse, take it to NCAT. Asking them to take responsibility for work that they did illegally is a prefectly reasonable request