You cannot install Web Server to a directory that contains an earlier version of Web Server. You can, however, migrate the existing installation after installing Web Server to a new directory.
Web Server can be installed as part of Java Enterprise System or as a standalone version.
In a standalone installation, all the necessary shared components such as NSS, NSPR are co-packaged with the Web Server installation files.
If you are installing Web Server as part of the Java ES suite, the Java ES installer installs all the shared components such as NSS and NSPR as separate packages and Web Server specific binaries as separate operating system dependent packages. Hence you need to download and install all the shared components patches and Web Server patches.
Visit Sun Solve. Download and install the latest Java ES Component Patches for the respective operating system.