If, by forks, you mean custom clients made for Sauerbraten, maps made in the original main version (not the SVN) can be played on certain custom clients like ComEd (this sites' version of Cube 2 Sauerbraten). There are some more custom clients out there, but right now I can't quite name them.
If you mean something else like Red Eclipse or Inexor, then officially... yeah, they will be incompatible. Those games uses a different process, map file and all. That, and they are not as popular as Sauerbraten. As a matter of fact, I can't think of any other cube 2 based game being more popular than Sauerbraten.
Now, making a total conversion for Cube 2? No fork will make anything smoother unless you understand the code behind it, although I believe Platinum Arts Sandbox attempted to do this.