You would usually need council approval to change windows. So the owner should have drawn up plans, put them to the OC for approval, and had them stamped with the common seal to lodge with the council to get a DA. Obviously as common property this would have had to be approved at a general meeting. Yes you would need a by-law to make it clear that the owner had ongoing responsibility for the windows.
So aside from anything else there is likely to be a breach of council requirements. The OC should also ask the owner about that, because if council approval hasn’t been obtained the council can require it to be changed.
Although the strata manager is no longer there, the onus is on the owner to satisfy the OC that the requisite approvals were obtained, and from the facts it seems they weren’t.