The fact that Amtrak has to even hint at shutting one of the tunnels shows how dramatic the issues are in the tunnels and the approaches from the west of NYP.
The eventual tunnel closure does not refer to the work performed this summer. It has been known for a long time that the damage to the aging tunnels during the Sandy storm event would ultimately mean the tubes would have to be shut down for repairs, but the plan has always been to do this work after the Gateway tunnel is operational. While it is possible something could be found or occur which would require the tunnels be shuttered before then - particularly if Gateway faces delays (likely funding) - that is not the intention.
While Amtrak will be affected, Jis is correct in that it is the commuter traffic which will take by far the greatest hit. Penn Station is drowning in commuter trains; This will eventually have to be addressed further than just Gateway and the Farley building station expansion.