If it works like the other versions of the Flashpoint story, it'll be pretty much that, with some fun glimpses into an alternate reality DCEU. At the end, Flash will restore the timeline 90% of the way, but some things will be different. That's where you could, conceivably, introduce a different Bruce or show that Superman never ended up dying, for example.
Of course, these movies don't typically serve as direct adaptations. So I don't expect it to be true to the Flashpoint storyline anymore than Civil War was to it's source material.