You need to run the ORDS setup again for the server you want to update.
java -jar ords.war setup
This will update everything for you, you will need to supply all the information though (servers, ports and passwords etc).
That worked with the previous 2.0 version of ORDS but, does not appear to work with the 3.X versions. Unless I am missing something. It never even prompts me for the various user names and passwords, e.g. APEX_PUBLIC_USER, etc.