If the TopologyMgr folder is in the Netsight directory on the server, and the jar files are there, then it hasn't been removed but is just not running, or it was messed up by Java. Have you tried deleting all of your java temporary files? Go into java Control panel in windows control panel and click settings and delete all of the files and then connect back to the URL and have Java reinstall everything?
Your JNLP file should contain the following lines:
https://yourURL:8443/Clients/plugins/TopologyMgr/JGo.jar"; download="eager" main="false"/> https://yourURL:8443/Clients/plugins/TopologyMgr/JGoLayout.jar"; download="eager" main="false"/>
https://yourURL:8443/Clients/plugins/TopologyMgr/JGoSVG.jar"; download="eager" main="false"/>
https://yourURL:8443/Clients/plugins/TopologyMgr/TopologyMgr.jar"; download="eager" main="false"/>