If you change configuration options or add images to an existing gallery, then you'll need to re-upload:
(1) The 'config.xml' file (which stores the configuration options and the image data).
(2) The new images (in the 'images' folder).
(3) The new thumbnails (in the 'thumbs' folder).

There will be no need to re-upload the 'jbcore' folder (this remains the same for all galleries) or the 'index.html' file (which contains the gallery's embedding code).

NB
You will need to re-upload the 'index.html' file (or change your gallery's embedding code) if you change the gallery dimensions or background color as these configuration options (galleryWidth, galleryHeight and backgroundColor) are set in the embedding code rather than the 'config.xml' file.