I’m calling this weekend — late night Friday, September 22 to early morning Monday, Swptember 25 — a “green light weekend” — as all trains serving local stations should be running in both directions. The only departure from the normal is that 2 trains will be on a reduced schedule: every 12 minutes. For those traveling to or from JFK, there will be no direct “train to the plane” service. You may need to splurge on a taxi.
The following work week — Monday, September 25 trough Friday, September 29 — late nights Monday to Tuesday through Thursday to Friday, 4 trains will not be serving Brooklyn in either direction. However, 3 trains will be making all Brooklyn 4 stops in both directions. On all late nights there will be no R trins running in either direction at Court Street or at Jay Street-MetroTech, but N trains should be running normally in both directions. Also, on late nights only, the same mishugas concerning travel to and from JFK, described above, applies.
Always check MTA Info for last minute changes in planned service or unplanned service changes that may affect local service or service on other parts of your trip, or for planned service changes that affect stations to or from which you may be traveling. You can also get real time service alerts: register here.