Discovery travelled into the future from a point of time in the 23rd century before any other changes. Unless we go with the idea that the timeline is continuing to evolve and time travel to the future takes into account all changes to a timeline in the years in-between, they would go into a future that's the future of the timeline that existed from the point they left.
I get where you ate going with this, but wouldn't that require that when looking back, no time travel took place in the intervening 900 years? And we know that isn't the case because there was a whole temporal war in the interim.