I think if the .jar does not get reloaded than it's probably a Trinidad bug (since during context restarts jars should be re-added - assuming Tomcat does this by default - I'm not sure) ... would be great to know details (in Trinidad's tracker) e.g. if the jar is named the same, how does the configuration look like (if any).
The other option would be to try out a rolling restart since than a brand new context is created - thus it should pick up anything that the context depends on from the file-system.
Please note that auto-reloading on file changes such as changing a .jar file even though might work with Tomcat is on purpose disabled in Trinidad - you need to "explicitly" (touch ...) to request a restart.