Sun Java Enterprise System 5 Release Notes for UNIX

After installing a component with the Java ES installer, you must use the uninstaller to uninstall (no bug number)

If you remove component packages or RPMs directly, the next time the installer is run, it may see a component as still being installed and not behave correctly.

Solution If you have already removed component packages or RPMs manually, you must still use the Java ES uninstaller to uninstall the component.