In the process of moving Subclipse to Github and setting up automated build and deploy we took the liberty of simplifying some of the packaging and moved around a couple of the plugins into the main Subclipse feature. Upgrade can fail if you have the features installed we removed since there is no new version to upgrade them to latest version. To fix the problem just uninstall the existing Subclipse features.

If you go to Help > About and then click on Installation Details look for the existing Subclipse and CollabNet features and then select them and choose Uninstall. After restarting Eclipse you should be able to re-install from the new update site without problem.