I have a .properties file in my application which contains dataSource properties. I set up a JNDI reference to this dataSource using the following code :
//
What you are trying to do is not going to work. J2EE applications are not allowed to modify the JNDI environment provided by the application server (J2EE spec, section 5.2.2) and the Tomcat JNDI documentation also states, that each web applications gets each own read-only JNDI environment. I'm not sure why binding/rebinding your datasource is not failing immediately and why it's working within the same web application, but even such application-internal usage of the JNDI environment is undocumented behaviour, which I would not rely on.