Using the examples of the VOY episode "Living Witness" and the NF comic "Double Time", is it possible that the Federation no longer exist in the future?
In "Living Witness", or at least those parts set in the future - in the 31st and ?33rd century - we see a planet in the Delta Quadrant that had no contact with the Federation since Voyager left. The lack of any Federation presence seem a bit strange to me given the current novelverse and possibly also Online. [I agree that it could be explained away by setting the future parts into the pre-"Future's End" timeline: Voyager and Earth destroyed in the 26th century...]
In "Double Time", there is an encounter with a ship belonging to the Enevian Empire in the 39th century. And this empire seem to have good chances at conquering the galaxy, which would be strange if the Federation still stood. [Although it could just said that they are just a "new" faction in the Temporal Cold War.]
I am open to any ideas or suggestions.