Tips
With Emby for Kodi 4.x, you should now have access to kodi.emby.media which contains some previous and always the latest build. This gives you an easy way to revert back to the previous version in case there's a bug, that is after reporting your issue (please).
From add-ons > install from zip
You can sync repair, update, remove individual libraries via Launching emby for kodi. Then opening the context menu on the library you want.
