After upgrading to Kibana 4.2.1 by extracting the archive and replacing the /opt/kibana directory, Marvel seems missing. Do I have to reinstall Marvel? And what about the licence?
The Kibana plugin files are kept in the installedPlugins directory in the root of Kibana, so if you replace Kibana, it will remove your installed plugins, such as Marvel. You will need to re-install Marvel for it to show up in Kibana's app switcher now. If you want to avoid having to do that in the future, you can try backing up the installedPlugins directory before replacing the Kibana files.
The License plugin is an Elasticsearch plugin, which has unrelated management to Kibana, so your license should be fine.
Thanks! I restored the marvel directory in the installedPlugins directory, restarted Kibana and it works fine again.