Hi Michelle,
It sounds like you're doing the right thing. When you create a new connection, org.jboss.remoting.AbstractInvoker.createSocketFactory() should call SSLSocketBuilder to get a new socket factory, and the new socket factory should be created with the new keystore. Hmmm.
How is your client configured? Have you looked at AbstractInvoker.createSocketFactory() to verify that the new socket factory is, in fact, being created by your SSLSocketBuilder.
-Ron