This last turn a new city (Diamantina) appeared in Brazil in the Terra Incognita, so it is there but not visible. I can drag-build a Depot there to build, and see the structure while in the econ interface.
This may be a bug, or may be an intentional mystery until the map is revealed at some later time. There have in the past been announced events in the terra incognita, and troops have moved through it (including the escape of troops teleported into the Amazon and the movement of relief supply columns).