One component that I'm maintaining at work uses a jar which combines original code, JSSE classes, and HttpClient (http://www.innovation.ch/java/HTTPClient/) classes. Yes, in one single jar. Someone built the jar 5 years ago and it hasn't been touched since.
In any case, we're moving the component to use Java 1.5 (instead of current 1.3.1), and I'm wondering if the JSSE classes in this jar could cause conflicts with their cousins from the 1.5 JDK/JRE.
You should remove the JSSE classes from the application as part of the move to 1.5. They may or may not cause problems, but in any case they're redundant. Maybe as part of the move you're considering breaking up that jar file into its constituent pieces anyway?