I read this story some time around 2001-2005 or so. I believe I read it online, however it was certainly of the variety that could be found in an anthology. I don’t remember many details other than the basic premise:
A large space ship or mobile space station full of humans has been in deep space for a long time, several dozen generations if my memory serves me. They are heading to a nearby star to colonize it on behalf of Earth. But Earth society has advanced dramatically in the hundreds (possibly thousands?) of years since their departure, and humanity has unlocked technology that allows them to manipulate the structure of space itself. The people onboard the ship watch in astonishment and dread as the very fabric of the universe is changed around them in the distance. They are still a long way from reaching their goal but are completely forgotten by their counterparts on Earth and have actually become obsolete, both in terms of their mission and their genetic makeup. The people on the ship have become aliens of a sort compared with what they believe the Earth humans have evolved into, although they only are able to infer this based on the fact that they watch the star system they are headed toward be colonized and transformed, just like their home solar system and many others in the sky.
It also seems to me that the people on the ship reach the conclusion that Earth humans have diverged from them physically and mentally based on either direct interaction or observation. The key point is that people on Earth have—through a combination of genetic meddling and mechanical augmentation—become individually capable of traversing the Galaxy in the form of large, conscious spacecraft. It is possible that the people on the voyaging ship only observe one of these cosmic ship-humans but I actually seem to remember that they make direct contact with one, and that it is completely uninterested in either helping them or even lingering long to talk to them and it quickly leaves them on their lonely course to the already colonized star system, still thousands of years distant.
I also half-remember a possible ending: The people on the ship decide that whatever Earth humanity has become is not something they wish to encounter again, and they change their ship’s course toward an even more distant star system in a dark part of the Galaxy where nothing from Earth has yet reached.