After a refactoring, say when you change the Controller path and the scaffolding is created at the new path, then menu.jspx retains the old links and isn't updated at all. When you remove these old folders after a successful refactoring, then it's still not updated.
You can exit and reenter Roo and nothing will happen.
The work around is to open menu.jspx and delete the whole menu, then exit Roo and start it again. Only then is there an update, that should have happened already when the scaffolding was updated.
I find this to be a recurring theme since Roo 1.0 at least in that monitoring doesn't seem to be active nor is there command to force an update of all scaffoldings including menu.jspx. There are similar issues with the conversion service bean too.
This kind of issue does impede the speed of development and is a nuisance that should be able to fix.