This is with:
Scala plugin version: 2.0.0.beta11-2_09-201110031011-3a97f5e
Eclipse version: 3.6.2.v201102101200

This is in a mixed java/scala project with circular dependencies between java and scala source.

I first create a java project and add my java source to the build path. I then right-click on the top level in the package explorer and do Scala -> Add Scala nature. I then add my Scala source directory to the build path. The project compiles okay. I then do a rename refactoring on a Scala class. The references in Scala files get updated, but not in the java files.

Likewise, if I rename a class or method in Java that is referenced by the Scala code, references in the Scala code are not updated.

Obviously, the rename refactoring would be a lot more useful if both these cases worked properly!