I think the flash-sideways will continue, but they will have knowledge of the Island time-line. That's how alt-Charlie knows he's supposed to die and alt-Desmond discovers Penny and yet still remembers the sideways-verse when he comes back to the Island-verse. But he only remembers when he comes back because he's the Constant,due to the explosion at the Island-verse Swan. And Eloise is a Constant, like him, for some reason--perhaps because she is connected to her son the way Desmond is linked to Penny.
^Reading that again, I don't know whether to laugh or go get an aspirin.