Uhh. What.
First of all, if all that happens, happens in "both" worlds, than you do not have two worlds, where one is 3d and one is 2d. You have a 2d world with two viewports. Unless you have some clever ways of implementing height despite being 2d. I think that early Doom game was a 2d map as in, you could not be at the same spot in a different elevation.
You can have the game logic and output it via the 2d engine or the 3d engine. But of course your game logic is dependent on user interface and what the player can do in response to what the player sees and there is a fundamentally different approach if you shift your point of view. Of course it is trivial if you just switch from isometric 3d view to "2d" top down view. You just shift the axis to have the 3d world be a 2d projection.
Secondly, what do you think a minimap or a full map is? ;-) If you do not deactivate controls, your map view is 2d.
I remember a game that could for some parts or all of it played in such a fashion. Hidden & Dangerous. You could switch to top down view from ego perspective.