As @Mark+P has stated, because of the fact that some filenames contain the shortname of the project, with the way that Paratext manages files, changing the shortname of a project requires rewriting the entire history of the project to make sure that Project History can display changes correctly.
In addition to this technical requirement, I think it’s also needed to keep people sane - imagine going to the S/R dialog and the names of some of your projects have suddenly changed without warning.
That being said, Paratext could, theoretically, handle changing a shortname without a massive rewrite of the entire history because Mercurial (Paratext’s history backend) does understand the concept of renaming files. Paratext, and possibly the Registry, just don’t currently handle it well.