But Daniels and his crew know what was "supposed" to happen and what wasn't. He said things like "this wasn't supposed to happen to the Enterprise" so in this time the Enterprise does exist and had a very important mission, despite there being no mention of this Enterprise in previous trek (although all other versions shown and mentioned, unless of course mankind names a new ship Enterprise in our real world, from tall ship through late TNG versions), so not mentioning something has very little basis on what is shown anymore.
The Expanse is being setup to be shutdown anyway, with the spheres causing it. I would bet that they are going to cop out in that since the expanse was destroyed (via destroying or shutting down the spheres) that they just aren't mentioned in later series. The Enterprise will just fly out of that area of space, because the expanse won't exist anymore.