Those of you who saw my Flatbush Avenue Terminal reconfiguration in this thread a while back, forget I said anything about it. Because I understand that Nostrand Avenue is far too narrow for the Flatbush Avenue Terminal itself to be four-tracks instead of two. Plus, I don't think there's a need for tail tracks south of the station either. Much cheaper for Brooklyn IRT trains to be stored at Livonia Avenue yard rather than building tail tracks south of Flatbush Avenue Terminal and/or east of Utica Avenue. Either way, as someone told me a while back in this thread, Flatbush Avenue Terminal was never intended to be a terminal. It was always meant to be extended, but it never had due to $$$. Therefore, Nostrand Junction (or Rogers Junction, I don't care which name is actually use, don't matter anyway) is all that needs to be reconfigured. Or should I say that it should have been just like the merging and diverging south of 59 Street-Columbus Circle from the get-go.
Therefore, in my world, the limited & runs to and from Utica/New Lots will continue to operate just like in the real world.