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When a new version is released, all you need to do to upgrade a gallery is replace the gallery's 'jbcore'. The gallery's configuration options (which are stored in the XML file or the embedding code) will be unaffected.
If you have many galleries, you can have them all share a single instance of a 'jbcore' folder by following the instructions here.
Then, when a new version is released, you can upgrade all your galleries at once by replacing a single 'jbcore' folder on your web server.
Alternatively, if each of your galleries has its own 'jbcore' folder, you could perhaps use the Python script that wspollack has written to automate the process of replacing multiple 'jbcore' folders on a web server. It can be found in this forum thread.
(Please note that this is an unofficial script written by a user rather than ourselves and you should use it at your own risk.)